HEADER TRANSCRIPTION 26-MAY-08 2VUK
TITLE STRUCTURE OF THE P53 CORE DOMAIN MUTANT Y220C BOUND TO THE STABILIZING
TITLE 2 SMALL-MOLECULE DRUG PHIKAN083
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: CELLULAR TUMOR ANTIGEN P53;
COMPND 3 CHAIN: A, B;
COMPND 4 FRAGMENT: DNA-BINDING DOMAIN, RESIDUES 94-312;
COMPND 5 SYNONYM: TUMOR SUPPRESSOR P53, PHOSPHOPROTEIN P53, ANTIGEN NY-CO-13,
COMPND 6 P53;
COMPND 7 ENGINEERED: YES;
COMPND 8 MUTATION: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 3 ORGANISM_COMMON: HUMAN;
SOURCE 4 ORGANISM_TAXID: 9606;
SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 6 EXPRESSION_SYSTEM_TAXID: 511693;
SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21
KEYWDS METAL BINDING, PHOSPHOPROTEIN, UBL CONJUGATION, ACTIVATOR, CELL
KEYWDS 2 CYCLE, ACETYLATION, METHYLATION, ZINC, CANCER, NUCLEUS, APOPTOSIS,
KEYWDS 3 CYTOPLASM, TUMOR SUPPRESSOR, VIRTUAL SCREENING, SECOND-SITE
KEYWDS 4 SUPPRESSOR MUTATION, COVALENT PROTEIN-RNA LINKAGE, SMALL-MOLECULE
KEYWDS 5 DRUG, ALTERNATIVE SPLICING, P53 DNA- BINDING DOMAIN, TRANSCRIPTION
KEYWDS 6 REGULATION, NUCLEAR PROTEIN, SURFACE CREVICE, DISEASE MUTATION,
KEYWDS 7 PROTEIN STABILIZATION, HOST-VIRUS INTERACTION, LI-FRAUMENI SYNDROME,
KEYWDS 8 ENDOPLASMIC RETICULUM, METAL-BINDING, ANTI-ONCOGENE, TRANSCRIPTION,
KEYWDS 9 SUPERSTABLE MUTANT, DNA-BINDING PROTEIN, DNA BINDING, DNA-BINDING,
KEYWDS 10 POLYMORPHISM, GLYCOPROTEIN
EXPDTA X-RAY DIFFRACTION
AUTHOR A.C.JOERGER,F.M.BOECKLER,A.R.FERSHT
REVDAT 6 13-DEC-23 2VUK 1 LINK
REVDAT 5 08-MAY-19 2VUK 1 REMARK
REVDAT 4 24-FEB-09 2VUK 1 VERSN
REVDAT 3 12-AUG-08 2VUK 1 JRNL
REVDAT 2 05-AUG-08 2VUK 1 JRNL
REVDAT 1 22-JUL-08 2VUK 0
JRNL AUTH F.M.BOECKLER,A.C.JOERGER,G.JAGGI,T.J.RUTHERFORD,
JRNL AUTH 2 D.B.VEPRINTSEV,A.R.FERSHT
JRNL TITL TARGETED RESCUE OF A DESTABILIZED MUTANT OF P53 BY AN IN
JRNL TITL 2 SILICO SCREENED DRUG.
JRNL REF PROC.NATL.ACAD.SCI.USA V. 105 10360 2008
JRNL REFN ISSN 0027-8424
JRNL PMID 18650397
JRNL DOI 10.1073/PNAS.0805326105
REMARK 1
REMARK 1 REFERENCE 1
REMARK 1 AUTH A.C.JOERGER,H.-C.ANG,A.R.FERSHT
REMARK 1 TITL STRUCTURAL BASIS FOR UNDERSTANDING ONCOGENIC P53 MUTATIONS
REMARK 1 TITL 2 AND DESIGNING RESCUE DRUGS
REMARK 1 REF PROC.NATL.ACAD.SCI.USA V. 103 15056 2006
REMARK 1 REFN ISSN 0027-8424
REMARK 1 PMID 17015838
REMARK 1 DOI 10.1073/PNAS.0607286103
REMARK 2
REMARK 2 RESOLUTION. 1.50 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : CNS 1.2
REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE-
REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU,
REMARK 3 : READ,RICE,SIMONSON,WARREN
REMARK 3
REMARK 3 REFINEMENT TARGET : NULL
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.50
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 65.10
REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL
REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL
REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL
REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 96.6
REMARK 3 NUMBER OF REFLECTIONS : 76025
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT
REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM
REMARK 3 R VALUE (WORKING SET) : 0.186
REMARK 3 FREE R VALUE : 0.208
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000
REMARK 3 FREE R VALUE TEST SET COUNT : NULL
REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL
REMARK 3
REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN.
REMARK 3 TOTAL NUMBER OF BINS USED : NULL
REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL
REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL
REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL
REMARK 3 BIN R VALUE (WORKING SET) : NULL
REMARK 3 BIN FREE R VALUE : NULL
REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL
REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL
REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 3066
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 20
REMARK 3 SOLVENT ATOMS : 434
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 13.80
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 15.90
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : NULL
REMARK 3 B22 (A**2) : NULL
REMARK 3 B33 (A**2) : NULL
REMARK 3 B12 (A**2) : NULL
REMARK 3 B13 (A**2) : NULL
REMARK 3 B23 (A**2) : NULL
REMARK 3
REMARK 3 ESTIMATED COORDINATE ERROR.
REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL
REMARK 3 ESD FROM SIGMAA (A) : NULL
REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL
REMARK 3
REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR.
REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL
REMARK 3 ESD FROM C-V SIGMAA (A) : NULL
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES.
REMARK 3 BOND LENGTHS (A) : 0.009
REMARK 3 BOND ANGLES (DEGREES) : 1.500
REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL
REMARK 3 IMPROPER ANGLES (DEGREES) : NULL
REMARK 3
REMARK 3 ISOTROPIC THERMAL MODEL : NULL
REMARK 3
REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA
REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL
REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL
REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL
REMARK 3
REMARK 3 BULK SOLVENT MODELING.
REMARK 3 METHOD USED : NULL
REMARK 3 KSOL : NULL
REMARK 3 BSOL : NULL
REMARK 3
REMARK 3 NCS MODEL : NULL
REMARK 3
REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT
REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL
REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL
REMARK 3
REMARK 3 PARAMETER FILE 1 : NULL
REMARK 3 TOPOLOGY FILE 1 : NULL
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 2VUK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 26-MAY-08.
REMARK 100 THE DEPOSITION ID IS D_1290036151.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 07-DEC-07
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 7.2
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : DIAMOND
REMARK 200 BEAMLINE : I04
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.9699
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : ADSC CCD
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL
REMARK 200 DATA SCALING SOFTWARE : NULL
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 76025
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500
REMARK 200 RESOLUTION RANGE LOW (A) : 65.100
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 96.6
REMARK 200 DATA REDUNDANCY : 5.600
REMARK 200 R MERGE (I) : 0.07000
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 17.7000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.58
REMARK 200 COMPLETENESS FOR SHELL (%) : 83.4
REMARK 200 DATA REDUNDANCY IN SHELL : 4.60
REMARK 200 R MERGE FOR SHELL (I) : 0.23000
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 5.600
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: CNS
REMARK 200 STARTING MODEL: PDB ENTRY 2J1X
REMARK 200
REMARK 200 REMARK: NONE
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 51.00
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.50
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: SITTING DROP VAPOR DIFFUSION AT 21
REMARK 280 DEGREE C. PROTEIN SOLUTION: 6 MG/ML PROTEIN IN 25 MM SODIUM
REMARK 280 PHOSPHATE PH 7.2, 150 MM KCL, 5 MM DTT. RESERVOIR BUFFER: 100 MM
REMARK 280 HEPES PH 7.2, 19 % PEG 4000, 5 MM DTT. CRYSTALS WERE SOAKED WITH
REMARK 280 10 MM PHIKAN083 IN CRYO BUFFER CONTAINING 100 MM HEPES PH 7.2,
REMARK 280 10 MM SODIUM PHOSPHATE PH 7.2, 19 % PEG 4000, 20 % GLYCEROL, 150
REMARK 280 MM KCL., VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -X+1/2,-Y,Z+1/2
REMARK 290 3555 -X,Y+1/2,-Z+1/2
REMARK 290 4555 X+1/2,-Y+1/2,-Z
REMARK 290
REMARK 290 WHERE NNN -> OPERATOR NUMBER
REMARK 290 MMM -> TRANSLATION VECTOR
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS
REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM
REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY
REMARK 290 RELATED MOLECULES.
REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 32.54650
REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 52.60350
REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 35.61700
REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 52.60350
REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 32.54650
REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 35.61700
REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000
REMARK 290
REMARK 290 REMARK: NULL
REMARK 300
REMARK 300 BIOMOLECULE: 1, 2
REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM
REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN
REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON
REMARK 300 BURIED SURFACE AREA.
REMARK 350
REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN
REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE
REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS
REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND
REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN.
REMARK 350
REMARK 350 BIOMOLECULE: 1
REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC
REMARK 350 SOFTWARE USED: PQS
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A
REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000
REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000
REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000
REMARK 350
REMARK 350 BIOMOLECULE: 2
REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC
REMARK 350 SOFTWARE USED: PQS
REMARK 350 APPLY THE FOLLOWING TO CHAINS: B
REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000
REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000
REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000
REMARK 400
REMARK 400 COMPOUND
REMARK 400 ENGINEERED RESIDUE IN CHAIN A, MET 133 TO LEU
REMARK 400 ENGINEERED RESIDUE IN CHAIN A, VAL 203 TO ALA
REMARK 400 ENGINEERED RESIDUE IN CHAIN A, TYR 220 TO CYS
REMARK 400 ENGINEERED RESIDUE IN CHAIN A, ASN 239 TO TYR
REMARK 400 ENGINEERED RESIDUE IN CHAIN A, ASN 268 TO ASP
REMARK 400 ENGINEERED RESIDUE IN CHAIN B, MET 133 TO LEU
REMARK 400 ENGINEERED RESIDUE IN CHAIN B, VAL 203 TO ALA
REMARK 400 ENGINEERED RESIDUE IN CHAIN B, TYR 220 TO CYS
REMARK 400 ENGINEERED RESIDUE IN CHAIN B, ASN 239 TO TYR
REMARK 400 ENGINEERED RESIDUE IN CHAIN B, ASN 268 TO ASP
REMARK 465
REMARK 465 MISSING RESIDUES
REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE
REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.)
REMARK 465
REMARK 465 M RES C SSSEQI
REMARK 465 SER A 94
REMARK 465 SER A 95
REMARK 465 LYS A 291
REMARK 465 LYS A 292
REMARK 465 GLY A 293
REMARK 465 GLU A 294
REMARK 465 PRO A 295
REMARK 465 HIS A 296
REMARK 465 HIS A 297
REMARK 465 GLU A 298
REMARK 465 LEU A 299
REMARK 465 PRO A 300
REMARK 465 PRO A 301
REMARK 465 GLY A 302
REMARK 465 SER A 303
REMARK 465 THR A 304
REMARK 465 LYS A 305
REMARK 465 ARG A 306
REMARK 465 ALA A 307
REMARK 465 LEU A 308
REMARK 465 PRO A 309
REMARK 465 ASN A 310
REMARK 465 ASN A 311
REMARK 465 THR A 312
REMARK 465 SER B 94
REMARK 465 LYS B 291
REMARK 465 LYS B 292
REMARK 465 GLY B 293
REMARK 465 GLU B 294
REMARK 465 PRO B 295
REMARK 465 HIS B 296
REMARK 465 HIS B 297
REMARK 465 GLU B 298
REMARK 465 LEU B 299
REMARK 465 PRO B 300
REMARK 465 PRO B 301
REMARK 465 GLY B 302
REMARK 465 SER B 303
REMARK 465 THR B 304
REMARK 465 LYS B 305
REMARK 465 ARG B 306
REMARK 465 ALA B 307
REMARK 465 LEU B 308
REMARK 465 PRO B 309
REMARK 465 ASN B 310
REMARK 465 ASN B 311
REMARK 465 THR B 312
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: TORSION ANGLES
REMARK 500
REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS:
REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2)
REMARK 500
REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI-
REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400
REMARK 500
REMARK 500 M RES CSSEQI PSI PHI
REMARK 500 LEU A 188 -42.18 -136.33
REMARK 500
REMARK 500 REMARK: NULL
REMARK 600
REMARK 600 HETEROGEN
REMARK 600
REMARK 600 1-(9-ETHYL-9H-CARBAZOL-3-YL)-N-METHYLMETHANAMINE (P83):
REMARK 600 STABILIZING SMALL-MOLECULE COMPOUND, PHIKAN083, WHICH
REMARK 600 BINDS TO THE MUTATION-INDUCED SURFACE CREVICE NEXT TO
REMARK 600 CYS220. PHIKAN083 WAS SOAKED INTO CRYSTALS OF T-P53C-Y220C
REMARK 600 AT A CONCENTRATION OF 10 MM. IN CHAIN B OF THE ASYMMETRIC
REMARK 600 UNIT, THERE IS UNAMBIGUOUS ELECTRON DENSITY FOR A
REMARK 600 PHIKAN083 MOLECULE BOUND TO THE MUTATION-INDUCED SURFACE
REMARK 600 CLEFT, WHEREAS THE POCKET IS PARTLY OCCUPIED IN CHAIN A.
REMARK 600 FOR THE CAVITY IN CHAIN A, WE OBSERVED SIGNIFICANT
REMARK 600 DIFFERENCE DENSITY HAVING CONTRIBUTIONS FROM PHIKAN083 IN
REMARK 600 THE SAME BINDING MODE AS IN CHAIN B BUT BOUND WITH A LOW
REMARK 600 OCCUPANCY, AND A NETWORK OF WATER MOLECULES AS OBSERVED IN
REMARK 600 THE UNBOUND STATE, CF. PDB ENTRY 2J1X. WE DID NOT INCLUDE
REMARK 600 THE LIGAND IN THE FINAL MODEL OF CHAIN A.
REMARK 620
REMARK 620 METAL COORDINATION
REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE):
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 ZN A1300 ZN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 CYS A 176 SG
REMARK 620 2 HIS A 179 ND1 105.2
REMARK 620 3 CYS A 238 SG 110.1 105.9
REMARK 620 4 CYS A 242 SG 111.9 106.0 116.8
REMARK 620 N 1 2 3
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 ZN B1300 ZN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 CYS B 176 SG
REMARK 620 2 HIS B 179 ND1 102.5
REMARK 620 3 CYS B 238 SG 110.2 108.4
REMARK 620 4 CYS B 242 SG 112.0 107.0 115.7
REMARK 620 N 1 2 3
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A1300
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B1300
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE P83 B1291
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 2BIQ RELATED DB: PDB
REMARK 900 HUMAN P53 CORE DOMAIN MUTANT T123A-M133L- H168R-V203A-N239Y-R249S-
REMARK 900 N268D
REMARK 900 RELATED ID: 1DT7 RELATED DB: PDB
REMARK 900 SOLUTION STRUCTURE OF THE C-TERMINAL NEGATIVE REGULATORY DOMAIN OF
REMARK 900 P53 IN A COMPLEX WITH CA2+-BOUND S100B(BB)
REMARK 900 RELATED ID: 2J1X RELATED DB: PDB
REMARK 900 HUMAN P53 CORE DOMAIN MUTANT M133L-V203A- Y220C-N239Y-N268D
REMARK 900 RELATED ID: 1UOL RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF THE HUMAN P53 CORE DOMAIN MUTANT M133L/V203A/
REMARK 900 N239Y/N268D AT 1 .9 A RESOLUTION.
REMARK 900 RELATED ID: 2B3G RELATED DB: PDB
REMARK 900 P53N (FRAGMENT 33-60) BOUND TO RPA70N
REMARK 900 RELATED ID: 2BIN RELATED DB: PDB
REMARK 900 HUMAN P53 CORE DOMAIN MUTANT M133L-H168R- V203A-N239Y-N268D
REMARK 900 RELATED ID: 1OLH RELATED DB: PDB
REMARK 900 P53 (OLIGOMERIZATION DOMAIN) (NMR, 35 STRUCTURES)
REMARK 900 RELATED ID: 1TSR RELATED DB: PDB
REMARK 900 P53 CORE DOMAIN IN COMPLEX WITH DEOXYRIBONUCLEIC ACID
REMARK 900 RELATED ID: 1PES RELATED DB: PDB
REMARK 900 TUMOR ANTIGEN P53 (TETRAMERIZATION DOMAIN) ( P53TET) (NMR,
REMARK 900 MINIMIZED AVERAGE STRUCTURE)
REMARK 900 RELATED ID: 2J21 RELATED DB: PDB
REMARK 900 HUMAN P53 CORE DOMAIN MUTANT M133L-V203A- N239Y-N268D-R282W
REMARK 900 RELATED ID: 2GS0 RELATED DB: PDB
REMARK 900 NMR STRUCTURE OF THE COMPLEX BETWEEN THE PH DOMAIN OF THETFB1
REMARK 900 SUBUNIT FROM TFIIH AND THE ACTIVATION DOMAIN OF P53
REMARK 900 RELATED ID: 2J0Z RELATED DB: PDB
REMARK 900 P53 TETRAMERIZATION DOMAIN WILD TYPE
REMARK 900 RELATED ID: 1C26 RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF P53 TETRAMERIZATION DOMAIN
REMARK 900 RELATED ID: 1SAL RELATED DB: PDB
REMARK 900 HIGH RESOLUTION SOLUTION NMR STRUCTURE OF THE OLIGOMERIZATION
REMARK 900 DOMAIN OF P53 BY MULTI- DIMENSIONAL NMR (SAD STRUCTURES)
REMARK 900 RELATED ID: 1KZY RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF THE 53BP1 BRCT REGION COMPLEXED TOTUMOR
REMARK 900 SUPPRESSOR P53
REMARK 900 RELATED ID: 1XQH RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF A TERNARY COMPLEX OF THEMETHYLTRANSFERASE SET9
REMARK 900 (ALSO KNOWN AS SET7 /9) WITH A P53PEPTIDE AND SAH
REMARK 900 RELATED ID: 2FEJ RELATED DB: PDB
REMARK 900 SOLUTION STRUCTURE OF HUMAN P53 DNA BINDING DOMAIN.
REMARK 900 RELATED ID: 2AHI RELATED DB: PDB
REMARK 900 STRUCTURAL BASIS OF DNA RECOGNITION BY P53 TETRAMERS(COMPLEX III)
REMARK 900 RELATED ID: 1A1U RELATED DB: PDB
REMARK 900 SOLUTION STRUCTURE DETERMINATION OF A P53 MUTANT DIMERIZATION
REMARK 900 DOMAIN, NMR, MINIMIZED AVERAGE STRUCTURE
REMARK 900 RELATED ID: 3SAK RELATED DB: PDB
REMARK 900 HIGH RESOLUTION SOLUTION NMR STRUCTURE OF THE OLIGOMERIZATION
REMARK 900 DOMAIN OF P53 BY MULTI- DIMENSIONAL NMR (SAC STRUCTURES)
REMARK 900 RELATED ID: 1SAF RELATED DB: PDB
REMARK 900 HIGH RESOLUTION SOLUTION NMR STRUCTURE OF THE OLIGOMERIZATION
REMARK 900 DOMAIN OF P53 BY MULTI- DIMENSIONAL NMR (SAD STRUCTURES)
REMARK 900 RELATED ID: 2BIO RELATED DB: PDB
REMARK 900 HUMAN P53 CORE DOMAIN MUTANT M133L-V203A- N239Y-R249S-N268D
REMARK 900 RELATED ID: 1SAG RELATED DB: PDB
REMARK 900 HIGH RESOLUTION SOLUTION NMR STRUCTURE OF THE OLIGOMERIZATION
REMARK 900 DOMAIN OF P53 BY MULTI- DIMENSIONAL NMR (SAC STRUCTURES)
REMARK 900 RELATED ID: 1OLG RELATED DB: PDB
REMARK 900 P53 (OLIGOMERIZATION DOMAIN) (NMR, MINIMIZED AVERAGE STRUCTURE)
REMARK 900 RELATED ID: 2J11 RELATED DB: PDB
REMARK 900 P53 TETRAMERIZATION DOMAIN MUTANT Y327S T329G Q331G
REMARK 900 RELATED ID: 2BIP RELATED DB: PDB
REMARK 900 HUMAN P53 CORE DOMAIN MUTANT M133L-H168R- V203A-N239Y-R249S-N268D
REMARK 900 RELATED ID: 1SAI RELATED DB: PDB
REMARK 900 HIGH RESOLUTION SOLUTION NMR STRUCTURE OF THE OLIGOMERIZATION
REMARK 900 DOMAIN OF P53 BY MULTI- DIMENSIONAL NMR (SAC STRUCTURES)
REMARK 900 RELATED ID: 1PET RELATED DB: PDB
REMARK 900 TUMOR ANTIGEN P53 (TETRAMERIZATION DOMAIN) ( P53TET) (NMR, 19
REMARK 900 STRUCTURES)
REMARK 900 RELATED ID: 2J1Y RELATED DB: PDB
REMARK 900 HUMAN P53 CORE DOMAIN MUTANT M133L-V203A- N239Y-G245S-N268D
REMARK 900 RELATED ID: 1JSP RELATED DB: PDB
REMARK 900 NMR STRUCTURE OF CBP BROMODOMAIN IN COMPLEX WITH P53 PEPTIDE
REMARK 900 RELATED ID: 1MA3 RELATED DB: PDB
REMARK 900 STRUCTURE OF A SIR2 ENZYME BOUND TO AN ACETYLATED P53PEPTIDE
REMARK 900 RELATED ID: 1AIE RELATED DB: PDB
REMARK 900 P53 TETRAMERIZATION DOMAIN CRYSTAL STRUCTURE
REMARK 900 RELATED ID: 2H1L RELATED DB: PDB
REMARK 900 THE STRUCTURE OF THE ONCOPROTEIN SV40 LARGE T ANTIGEN ANDP53 TUMOR
REMARK 900 SUPPRESSOR COMPLEX
REMARK 900 RELATED ID: 1SAJ RELATED DB: PDB
REMARK 900 HIGH RESOLUTION SOLUTION NMR STRUCTURE OF THE OLIGOMERIZATION
REMARK 900 DOMAIN OF P53 BY MULTI- DIMENSIONAL NMR (SAD STRUCTURES)
REMARK 900 RELATED ID: 1TUP RELATED DB: PDB
REMARK 900 TUMOR SUPPRESSOR P53 COMPLEXED WITH DEOXYRIBONUCLEIC ACID
REMARK 900 RELATED ID: 1HS5 RELATED DB: PDB
REMARK 900 NMR SOLUTION STRUCTURE OF DESIGNED P53 DIMER
REMARK 900 RELATED ID: 2ATA RELATED DB: PDB
REMARK 900 STRUCTURAL BASIS OF DNA RECOGNITION BY P53 TETRAMERS(COMPLEX II)
REMARK 900 RELATED ID: 1YCQ RELATED DB: PDB
REMARK 900 XENOPUS LAEVIS MDM2 BOUND TO THE TRANSACTIVATION DOMAIN OF HUMAN P53
REMARK 900 RELATED ID: 1GZH RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF THE BRCT DOMAINS OF HUMAN 53BP1 BOUND TO THE
REMARK 900 P53 TUMOR SUPRESSOR
REMARK 900 RELATED ID: 1SAH RELATED DB: PDB
REMARK 900 HIGH RESOLUTION SOLUTION NMR STRUCTURE OF THE OLIGOMERIZATION
REMARK 900 DOMAIN OF P53 BY MULTI- DIMENSIONAL NMR (SAD STRUCTURES)
REMARK 900 RELATED ID: 2BIM RELATED DB: PDB
REMARK 900 HUMAN P53 CORE DOMAIN MUTANT M133L-V203A- N239Y-N268D-R273H
REMARK 900 RELATED ID: 1YCR RELATED DB: PDB
REMARK 900 MDM2 BOUND TO THE TRANSACTIVATION DOMAIN OF P53
REMARK 900 RELATED ID: 2J10 RELATED DB: PDB
REMARK 900 P53 TETRAMERIZATION DOMAIN MUTANT T329F Q331K
REMARK 900 RELATED ID: 2ADY RELATED DB: PDB
REMARK 900 STRUCTURAL BASIS OF DNA RECOGNITION BY P53 TETRAMERS(COMPLEX IV)
REMARK 900 RELATED ID: 1SAK RELATED DB: PDB
REMARK 900 HIGH RESOLUTION SOLUTION NMR STRUCTURE OF THE OLIGOMERIZATION
REMARK 900 DOMAIN OF P53 BY MULTI- DIMENSIONAL NMR (SAC STRUCTURES)
REMARK 900 RELATED ID: 2J1Z RELATED DB: PDB
REMARK 900 HUMAN P53 CORE DOMAIN MUTANT M133L-V203A- N239Y-N268D-F270L
REMARK 900 RELATED ID: 1SAE RELATED DB: PDB
REMARK 900 HIGH RESOLUTION SOLUTION NMR STRUCTURE OF THE OLIGOMERIZATION
REMARK 900 DOMAIN OF P53 BY MULTI- DIMENSIONAL NMR (SAC STRUCTURES)
REMARK 900 RELATED ID: 2AC0 RELATED DB: PDB
REMARK 900 STRUCTURAL BASIS OF DNA RECOGNITION BY P53 TETRAMERS(COMPLEX I)
REMARK 900 RELATED ID: 1YCS RELATED DB: PDB
REMARK 900 P53-53BP2 COMPLEX
REMARK 900 RELATED ID: 2J20 RELATED DB: PDB
REMARK 900 HUMAN P53 CORE DOMAIN MUTANT M133L-V203A- N239Y-N268D-R273C
REMARK 900 RELATED ID: 1H26 RELATED DB: PDB
REMARK 900 CDK2/CYCLINA IN COMPLEX WITH AN 11-RESIDUE RECRUITMENT PEPTIDE FROM
REMARK 900 P53
REMARK 900 RELATED ID: 2J1W RELATED DB: PDB
REMARK 900 HUMAN P53 CORE DOMAIN MUTANT M133L-V143A- V203A-N239Y-N268D
DBREF 2VUK A 94 312 UNP P04637 P53_HUMAN 94 312
DBREF 2VUK B 94 312 UNP P04637 P53_HUMAN 94 312
SEQADV 2VUK LEU A 133 UNP P04637 MET 133 ENGINEERED MUTATION
SEQADV 2VUK ALA A 203 UNP P04637 VAL 203 ENGINEERED MUTATION
SEQADV 2VUK CYS A 220 UNP P04637 TYR 220 ENGINEERED MUTATION
SEQADV 2VUK TYR A 239 UNP P04637 ASN 239 ENGINEERED MUTATION
SEQADV 2VUK ASP A 268 UNP P04637 ASN 268 ENGINEERED MUTATION
SEQADV 2VUK LEU B 133 UNP P04637 MET 133 ENGINEERED MUTATION
SEQADV 2VUK ALA B 203 UNP P04637 VAL 203 ENGINEERED MUTATION
SEQADV 2VUK CYS B 220 UNP P04637 TYR 220 ENGINEERED MUTATION
SEQADV 2VUK TYR B 239 UNP P04637 ASN 239 ENGINEERED MUTATION
SEQADV 2VUK ASP B 268 UNP P04637 ASN 268 ENGINEERED MUTATION
SEQRES 1 A 219 SER SER SER VAL PRO SER GLN LYS THR TYR GLN GLY SER
SEQRES 2 A 219 TYR GLY PHE ARG LEU GLY PHE LEU HIS SER GLY THR ALA
SEQRES 3 A 219 LYS SER VAL THR CYS THR TYR SER PRO ALA LEU ASN LYS
SEQRES 4 A 219 LEU PHE CYS GLN LEU ALA LYS THR CYS PRO VAL GLN LEU
SEQRES 5 A 219 TRP VAL ASP SER THR PRO PRO PRO GLY THR ARG VAL ARG
SEQRES 6 A 219 ALA MET ALA ILE TYR LYS GLN SER GLN HIS MET THR GLU
SEQRES 7 A 219 VAL VAL ARG ARG CYS PRO HIS HIS GLU ARG CYS SER ASP
SEQRES 8 A 219 SER ASP GLY LEU ALA PRO PRO GLN HIS LEU ILE ARG VAL
SEQRES 9 A 219 GLU GLY ASN LEU ARG ALA GLU TYR LEU ASP ASP ARG ASN
SEQRES 10 A 219 THR PHE ARG HIS SER VAL VAL VAL PRO CYS GLU PRO PRO
SEQRES 11 A 219 GLU VAL GLY SER ASP CYS THR THR ILE HIS TYR ASN TYR
SEQRES 12 A 219 MET CYS TYR SER SER CYS MET GLY GLY MET ASN ARG ARG
SEQRES 13 A 219 PRO ILE LEU THR ILE ILE THR LEU GLU ASP SER SER GLY
SEQRES 14 A 219 ASN LEU LEU GLY ARG ASP SER PHE GLU VAL ARG VAL CYS
SEQRES 15 A 219 ALA CYS PRO GLY ARG ASP ARG ARG THR GLU GLU GLU ASN
SEQRES 16 A 219 LEU ARG LYS LYS GLY GLU PRO HIS HIS GLU LEU PRO PRO
SEQRES 17 A 219 GLY SER THR LYS ARG ALA LEU PRO ASN ASN THR
SEQRES 1 B 219 SER SER SER VAL PRO SER GLN LYS THR TYR GLN GLY SER
SEQRES 2 B 219 TYR GLY PHE ARG LEU GLY PHE LEU HIS SER GLY THR ALA
SEQRES 3 B 219 LYS SER VAL THR CYS THR TYR SER PRO ALA LEU ASN LYS
SEQRES 4 B 219 LEU PHE CYS GLN LEU ALA LYS THR CYS PRO VAL GLN LEU
SEQRES 5 B 219 TRP VAL ASP SER THR PRO PRO PRO GLY THR ARG VAL ARG
SEQRES 6 B 219 ALA MET ALA ILE TYR LYS GLN SER GLN HIS MET THR GLU
SEQRES 7 B 219 VAL VAL ARG ARG CYS PRO HIS HIS GLU ARG CYS SER ASP
SEQRES 8 B 219 SER ASP GLY LEU ALA PRO PRO GLN HIS LEU ILE ARG VAL
SEQRES 9 B 219 GLU GLY ASN LEU ARG ALA GLU TYR LEU ASP ASP ARG ASN
SEQRES 10 B 219 THR PHE ARG HIS SER VAL VAL VAL PRO CYS GLU PRO PRO
SEQRES 11 B 219 GLU VAL GLY SER ASP CYS THR THR ILE HIS TYR ASN TYR
SEQRES 12 B 219 MET CYS TYR SER SER CYS MET GLY GLY MET ASN ARG ARG
SEQRES 13 B 219 PRO ILE LEU THR ILE ILE THR LEU GLU ASP SER SER GLY
SEQRES 14 B 219 ASN LEU LEU GLY ARG ASP SER PHE GLU VAL ARG VAL CYS
SEQRES 15 B 219 ALA CYS PRO GLY ARG ASP ARG ARG THR GLU GLU GLU ASN
SEQRES 16 B 219 LEU ARG LYS LYS GLY GLU PRO HIS HIS GLU LEU PRO PRO
SEQRES 17 B 219 GLY SER THR LYS ARG ALA LEU PRO ASN ASN THR
HET ZN A1300 1
HET P83 B1291 18
HET ZN B1300 1
HETNAM ZN ZINC ION
HETNAM P83 1-(9-ETHYL-9H-CARBAZOL-3-YL)-N-METHYLMETHANAMINE
FORMUL 3 ZN 2(ZN 2+)
FORMUL 4 P83 C16 H18 N2
FORMUL 6 HOH *434(H2 O)
HELIX 1 1 GLN A 165 MET A 169 5 5
HELIX 2 2 HIS A 178 CYS A 182 5 5
HELIX 3 3 CYS A 277 ARG A 290 1 14
HELIX 4 4 HIS B 178 CYS B 182 5 5
HELIX 5 5 CYS B 277 ARG B 290 1 14
SHEET 1 AA 4 ARG A 110 GLY A 112 0
SHEET 2 AA 4 CYS A 141 TRP A 146 -1 O GLN A 144 N GLY A 112
SHEET 3 AA 4 THR A 230 TYR A 236 -1 O THR A 230 N LEU A 145
SHEET 4 AA 4 ILE A 195 VAL A 197 -1 O ARG A 196 N ASN A 235
SHEET 1 AB 7 CYS A 124 SER A 127 0
SHEET 2 AB 7 LYS A 132 CYS A 135 -1 O LYS A 132 N SER A 127
SHEET 3 AB 7 LEU A 264 VAL A 274 1 O GLU A 271 N LEU A 133
SHEET 4 AB 7 ILE A 251 GLU A 258 -1 O ILE A 251 N VAL A 272
SHEET 5 AB 7 ARG A 156 TYR A 163 -1 O ARG A 156 N GLU A 258
SHEET 6 AB 7 HIS A 214 PRO A 219 -1 O VAL A 216 N ALA A 159
SHEET 7 AB 7 GLU A 204 ASP A 207 -1 O GLU A 204 N VAL A 217
SHEET 1 BA 4 ARG B 110 GLY B 112 0
SHEET 2 BA 4 CYS B 141 TRP B 146 -1 O GLN B 144 N GLY B 112
SHEET 3 BA 4 THR B 230 TYR B 236 -1 O THR B 230 N LEU B 145
SHEET 4 BA 4 ILE B 195 VAL B 197 -1 O ARG B 196 N ASN B 235
SHEET 1 BB 7 CYS B 124 SER B 127 0
SHEET 2 BB 7 LYS B 132 CYS B 135 -1 O LYS B 132 N SER B 127
SHEET 3 BB 7 LEU B 264 VAL B 274 1 O GLU B 271 N LEU B 133
SHEET 4 BB 7 ILE B 251 GLU B 258 -1 O ILE B 251 N VAL B 272
SHEET 5 BB 7 ARG B 156 TYR B 163 -1 O ARG B 156 N GLU B 258
SHEET 6 BB 7 HIS B 214 PRO B 219 -1 O VAL B 216 N ALA B 159
SHEET 7 BB 7 GLU B 204 ASP B 207 -1 O GLU B 204 N VAL B 217
LINK SG CYS A 176 ZN ZN A1300 1555 1555 2.33
LINK ND1 HIS A 179 ZN ZN A1300 1555 1555 2.03
LINK SG CYS A 238 ZN ZN A1300 1555 1555 2.33
LINK SG CYS A 242 ZN ZN A1300 1555 1555 2.31
LINK SG CYS B 176 ZN ZN B1300 1555 1555 2.33
LINK ND1 HIS B 179 ZN ZN B1300 1555 1555 2.00
LINK SG CYS B 238 ZN ZN B1300 1555 1555 2.33
LINK SG CYS B 242 ZN ZN B1300 1555 1555 2.33
SITE 1 AC1 4 CYS A 176 HIS A 179 CYS A 238 CYS A 242
SITE 1 AC2 4 CYS B 176 HIS B 179 CYS B 238 CYS B 242
SITE 1 AC3 9 LEU B 145 VAL B 147 THR B 150 CYS B 220
SITE 2 AC3 9 GLU B 221 PRO B 222 PRO B 223 ASP B 228
SITE 3 AC3 9 THR B 230
CRYST1 65.093 71.234 105.207 90.00 90.00 90.00 P 21 21 21 8
ORIGX1 1.000000 0.000000 0.000000 0.00000
ORIGX2 0.000000 1.000000 0.000000 0.00000
ORIGX3 0.000000 0.000000 1.000000 0.00000
SCALE1 0.015363 0.000000 0.000000 0.00000
SCALE2 0.000000 0.014038 0.000000 0.00000
SCALE3 0.000000 0.000000 0.009505 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
