HEADER HYDROLASE/HYDROLASE INHIBITOR 29-SEP-05 2C2O
TITLE CRYSTAL STRUCTURES OF CASPASE-3 IN COMPLEX WITH AZA-PEPTIDE MICHAEL
TITLE 2 ACCEPTOR INHIBITORS.
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: CASPASE-3 SUBUNIT P17;
COMPND 3 CHAIN: A;
COMPND 4 FRAGMENT: ALPHA SUBUNIT, RESIDUES 29-175;
COMPND 5 EC: 3.4.22.-;
COMPND 6 ENGINEERED: YES;
COMPND 7 MOL_ID: 2;
COMPND 8 MOLECULE: CASPASE-3 SUBUNIT P12;
COMPND 9 CHAIN: B;
COMPND 10 FRAGMENT: BETA SUBUNIT, RESIDUES 176-277;
COMPND 11 EC: 3.4.22.-;
COMPND 12 ENGINEERED: YES;
COMPND 13 MOL_ID: 3;
COMPND 14 MOLECULE: AZA-PEPTIDE INHIBITOR (5S, 8R, 11S)-14-{4-[BENZYL(METHYL)
COMPND 15 AMINO]-4-OXOBUTANOYL}-8-(2-CARBOXYETHYL)-5-(CARBOXYMETHYL)-11-(1-
COMPND 16 METHYLETHYL)-3,6,9,12-TETRAOXO-1-PHENYL-2-OXA-4,7,10,13,14-
COMPND 17 PENTAAZAHEXADECAN-16-OIC ACID;
COMPND 18 CHAIN: C;
COMPND 19 ENGINEERED: 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: 469008;
SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) (STRATAGENE);
SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET11D (NOVAGEN);
SOURCE 10 MOL_ID: 2;
SOURCE 11 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 12 ORGANISM_COMMON: HUMAN;
SOURCE 13 ORGANISM_TAXID: 9606;
SOURCE 14 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 15 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE 16 MOL_ID: 3;
SOURCE 17 SYNTHETIC: YES;
SOURCE 18 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT;
SOURCE 19 ORGANISM_TAXID: 32630
KEYWDS APOPTOSIS, HYDROLASE-HYDROLASE INHIBITOR COMPLEX, CYSTEINE-PROTEASE,
KEYWDS 2 ICE, TETRAMER, THIOL PROTEASE, ZYMOGEN, CPP32, YAMA, AZA-PEPTIDE,
KEYWDS 3 MICHAEL ACCEPTOR, AZA-ASP, CLAN CD
EXPDTA X-RAY DIFFRACTION
AUTHOR R.GANESAN,S.JELAKOVIC,O.D.EKICI,Z.Z.LI,K.E.JAMES,J.L.ASGIAN,
AUTHOR 2 A.CAMPBELL,J.MIKOLAJCZYK,G.S.SALVESEN,M.G.GRUETTER,J.C.POWERS
REVDAT 6 15-NOV-23 2C2O 1 LINK ATOM
REVDAT 5 28-JUN-17 2C2O 1 REMARK
REVDAT 4 08-FEB-17 2C2O 1 SOURCE
REVDAT 3 13-JUL-11 2C2O 1 VERSN
REVDAT 2 24-FEB-09 2C2O 1 VERSN
REVDAT 1 20-SEP-06 2C2O 0
JRNL AUTH O.D.EKICI,Z.Z.LI,A.J.CAMPBELL,K.E.JAMES,J.L.ASGIAN,
JRNL AUTH 2 J.MIKOLAJCZYK,G.S.SALVESEN,R.GANESAN,S.JELAKOVIC,
JRNL AUTH 3 M.G.GRUTTER,J.C.POWERS
JRNL TITL DESIGN, SYNTHESIS, AND EVALUATION OF AZA-PEPTIDE MICHAEL
JRNL TITL 2 ACCEPTORS AS SELECTIVE AND POTENT INHIBITORS OF CASPASES-2,
JRNL TITL 3 -3, -6, -7, -8, -9, AND - 10.
JRNL REF J.MED.CHEM. V. 49 5728 2006
JRNL REFN ISSN 0022-2623
JRNL PMID 16970398
JRNL DOI 10.1021/JM0601405
REMARK 2
REMARK 2 RESOLUTION. 2.45 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : CNS 1.1
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) : 2.45
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.55
REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000
REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1590597.210
REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL
REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.4
REMARK 3 NUMBER OF REFLECTIONS : 10094
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) : 0.168
REMARK 3 FREE R VALUE : 0.215
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.300
REMARK 3 FREE R VALUE TEST SET COUNT : 1040
REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.007
REMARK 3
REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN.
REMARK 3 TOTAL NUMBER OF BINS USED : 6
REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.45
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.60
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.20
REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1457
REMARK 3 BIN R VALUE (WORKING SET) : 0.2020
REMARK 3 BIN FREE R VALUE : 0.2630
REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 9.00
REMARK 3 BIN FREE R VALUE TEST SET COUNT : 144
REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.022
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 2051
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 0
REMARK 3 SOLVENT ATOMS : 149
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 22.00
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.00
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : 1.05000
REMARK 3 B22 (A**2) : 4.11000
REMARK 3 B33 (A**2) : -5.15000
REMARK 3 B12 (A**2) : 0.00000
REMARK 3 B13 (A**2) : 0.00000
REMARK 3 B23 (A**2) : 0.00000
REMARK 3
REMARK 3 ESTIMATED COORDINATE ERROR.
REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.21
REMARK 3 ESD FROM SIGMAA (A) : 0.21
REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00
REMARK 3
REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR.
REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.29
REMARK 3 ESD FROM C-V SIGMAA (A) : 0.30
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES.
REMARK 3 BOND LENGTHS (A) : 0.006
REMARK 3 BOND ANGLES (DEGREES) : 1.200
REMARK 3 DIHEDRAL ANGLES (DEGREES) : 22.90
REMARK 3 IMPROPER ANGLES (DEGREES) : 0.620
REMARK 3
REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED
REMARK 3
REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA
REMARK 3 MAIN-CHAIN BOND (A**2) : 1.200 ; 1.500
REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.930 ; 2.000
REMARK 3 SIDE-CHAIN BOND (A**2) : 2.160 ; 2.000
REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.070 ; 2.500
REMARK 3
REMARK 3 BULK SOLVENT MODELING.
REMARK 3 METHOD USED : FLAT MODEL
REMARK 3 KSOL : 0.36
REMARK 3 BSOL : 37.18
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 : PROTEIN_REP.PARAM
REMARK 3 PARAMETER FILE 2 : WATER.PARAM
REMARK 3 PARAMETER FILE 3 : NULL
REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP
REMARK 3 TOPOLOGY FILE 2 : NULL
REMARK 3 TOPOLOGY FILE 3 : NULL
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: MISSING RESIDUE CHAIN A, ASP 175
REMARK 3 CLONING ARTIFACT ADDITIONAL AMINO ACID CHAIN B, ALA 175
REMARK 4
REMARK 4 2C2O COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 29-SEP-05.
REMARK 100 THE DEPOSITION ID IS D_1290025821.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 04-JAN-05
REMARK 200 TEMPERATURE (KELVIN) : 100.0
REMARK 200 PH : 4.75
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : N
REMARK 200 RADIATION SOURCE : ROTATING ANODE
REMARK 200 BEAMLINE : NULL
REMARK 200 X-RAY GENERATOR MODEL : ENRAF-NONIUS FR591
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : IMAGE PLATE
REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM
REMARK 200 DATA SCALING SOFTWARE : SCALA
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10094
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.450
REMARK 200 RESOLUTION RANGE LOW (A) : 20.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2
REMARK 200 DATA REDUNDANCY : 5.800
REMARK 200 R MERGE (I) : 0.08000
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 19.6000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.45
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.58
REMARK 200 COMPLETENESS FOR SHELL (%) : 95.8
REMARK 200 DATA REDUNDANCY IN SHELL : 5.40
REMARK 200 R MERGE FOR SHELL (I) : 0.24000
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 7.000
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: OTHER
REMARK 200 SOFTWARE USED: NULL
REMARK 200 STARTING MODEL: NULL
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 46.00
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.28
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: PEG6000, 100 MM SODIUM CITRATE PH 4.75
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 2 2
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -X,-Y,Z
REMARK 290 3555 -X,Y,-Z
REMARK 290 4555 X,-Y,-Z
REMARK 290 5555 X+1/2,Y+1/2,Z+1/2
REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2
REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2
REMARK 290 8555 X+1/2,-Y+1/2,-Z+1/2
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 0.00000
REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000
REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000
REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 33.20100
REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 41.74550
REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 48.17800
REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 33.20100
REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 41.74550
REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 48.17800
REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 33.20100
REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 41.74550
REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 48.17800
REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 33.20100
REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 41.74550
REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 48.17800
REMARK 290
REMARK 290 REMARK: NULL
REMARK 300
REMARK 300 BIOMOLECULE: 1
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: HEXAMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: HEXAMERIC
REMARK 350 SOFTWARE USED: PQS
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C
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 BIOMT1 2 -1.000000 0.000000 0.000000 66.40200
REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000
REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 96.35600
REMARK 400
REMARK 400 COMPOUND
REMARK 400 THE INITIAL LIGAND USED IN THE EXPERIMENT WAS CBZ-DEVAD-CH=CH-
REMARK 400 CON(CH3)BZL, INDICATED AS 18O IN THE PRIMARY PUBLICATION. UPON
REMARK 400 REACTION, THE DOUBLE BOND OPENED UP AND FORMED A COVALENT BOND
REMARK 400 BETWEEN ATOM C10 OF RESIDUE MX3 5 OF CHAIN C AND ATOM SG OF CYS 163
REMARK 400 OF CHAIN A.
REMARK 400
REMARK 400 THE CBZ-ASP-GLU-VAL-AASP-CHCH-CON(CH3)CH2PH IS PEPTIDE-LIKE, A
REMARK 400 MEMBER OF INHIBITOR CLASS.
REMARK 400
REMARK 400 GROUP: 1
REMARK 400 NAME: CBZ-ASP-GLU-VAL-AASP-CHCH-CON(CH3)CH2PH
REMARK 400 CHAIN: C
REMARK 400 COMPONENT_1: PEPTIDE LIKE POLYMER
REMARK 400 DESCRIPTION: NULL
REMARK 470
REMARK 470 MISSING ATOM
REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER;
REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER;
REMARK 470 I=INSERTION CODE):
REMARK 470 M RES CSSEQI ATOMS
REMARK 470 ASP A 175 CA C O CB CG OD1 OD2
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: CLOSE CONTACTS
REMARK 500
REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC
REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15
REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A
REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375
REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE
REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS.
REMARK 500
REMARK 500 DISTANCE CUTOFF:
REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS
REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS
REMARK 500
REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE
REMARK 500 OE2 GLU A 123 OE2 GLU A 123 2665 2.18
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: COVALENT BOND ANGLES
REMARK 500
REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES
REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE
REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1)
REMARK 500
REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999
REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996
REMARK 500
REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3
REMARK 500 VAL C 4 O - C - N ANGL. DEV. = -14.0 DEGREES
REMARK 500
REMARK 500 REMARK: NULL
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 LYS A 82 30.86 75.25
REMARK 500 SER A 120 -175.73 -174.68
REMARK 500 ASP B 192 31.12 72.68
REMARK 500 LYS B 229 -31.82 -141.53
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY
REMARK 500
REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY
REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER
REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME;
REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER;
REMARK 500 I=INSERTION CODE).
REMARK 500
REMARK 500 M RES CSSEQI ANGLE
REMARK 500 VAL C 4 18.96
REMARK 500
REMARK 500 REMARK: NULL
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR CHAIN C OF AZA-PEPTIDE
REMARK 800 INHIBITOR (5S,8R,11S)-14-{4-[BENZYL(METHYL)AMINO]-4-OXOBUTANOYL}-
REMARK 800 8-(2-CARBOXYETHYL)-5-(CARBOXYMETHYL)-11-(1-METHYLETHYL)-3,6,9,12-
REMARK 800 TETRAOXO-1-PHENYL-2-OXA-4,7,10,13,14-PENTAAZAHEXADECAN-16-OIC
REMARK 800 ACID
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 1CP3 RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF THE COMPLEX OF APOPAIN WITH THE TETRAPEPTIDE
REMARK 900 INHIBITOR ACE-DVAD- FMC
REMARK 900 RELATED ID: 1GFW RELATED DB: PDB
REMARK 900 THE 2.8 ANGSTROM CRYSTAL STRUCTURE OF CASPASE-3 (APOPAIN ORCPP32)IN
REMARK 900 COMPLEX WITH AN ISATIN SULFONAMIDE INHIBITOR.
REMARK 900 RELATED ID: 1I3O RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF THE COMPLEX OF XIAP- BIR2 AND CASPASE 3
REMARK 900 RELATED ID: 1NME RELATED DB: PDB
REMARK 900 STRUCTURE OF CASP-3 WITH TETHERED SALICYLATE
REMARK 900 RELATED ID: 1NMQ RELATED DB: PDB
REMARK 900 EXTENDEND TETHERING: IN SITU ASSEMBLY OF INHIBITORS
REMARK 900 RELATED ID: 1NMS RELATED DB: PDB
REMARK 900 CASPASE-3 TETHERED TO IRREVERSIBLE INHIBITOR
REMARK 900 RELATED ID: 1PAU RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF THE COMPLEX OF APOPAIN WITH THE TETRAPEPTIDE
REMARK 900 ALDEHYDE INHIBITOR AC -DEVD-CHO
REMARK 900 RELATED ID: 1QX3 RELATED DB: PDB
REMARK 900 CONFORMATIONAL RESTRICTIONS IN THE ACTIVE SITE OFUNLIGANDED HUMAN
REMARK 900 CASPASE-3
REMARK 900 RELATED ID: 1RE1 RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF CASPASE-3 WITH A NICOTINIC ACIDALDEHYDE
REMARK 900 INHIBITOR
REMARK 900 RELATED ID: 1RHJ RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF THE COMPLEX OF CASPASE -3 WITH APRYAZINONE
REMARK 900 INHIBITOR
REMARK 900 RELATED ID: 1RHK RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF THE COMPLEX OF CASPASE -3 WITH A PHENYL-PROPYL-
REMARK 900 KETONE INHIBITOR
REMARK 900 RELATED ID: 1RHM RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF THE COMPLEX OF CASPASE -3 WITH ANICOTINIC ACID
REMARK 900 ALDEHYDE INHIBITOR
REMARK 900 RELATED ID: 1RHQ RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF THE COMPLEX OF CASPASE -3 WITH
REMARK 900 ABROMOMETHOXYPHENYL INHIBITOR
REMARK 900 RELATED ID: 1RHR RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF THE COMPLEX OF CASPASE -3 WITH ACINNAMIC ACID
REMARK 900 METHYL ESTER INHIBITOR
REMARK 900 RELATED ID: 1RHU RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF THE COMPLEX OF CASPASE -3 WITH A 5,6,
REMARK 900 7TRICYCLIC PEPTIDOMIMETIC INHIBITOR
REMARK 900 RELATED ID: 2C1E RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURES OF CASPASE-3 IN COMPLEX WITH AZA-PEPTIDE MICHAEL
REMARK 900 ACCEPTOR INHIBITORS.
REMARK 900 RELATED ID: 2C2K RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURES OF CASPASE-3 IN COMPLEX WITH AZA-PEPTIDE MICHAEL
REMARK 900 ACCEPTOR INHIBITORS.
REMARK 900 RELATED ID: 2C2M RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURES OF CASPASE-3 IN COMPLEX WITH AZA-PEPTIDE MICHAEL
REMARK 900 ACCEPTOR INHIBITORS.
REMARK 900 RELATED ID: 2CDR RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURES OF CASPASE-3 IN COMPLEX WITH AZA-PEPTIDE EPOXIDE
REMARK 900 INHIBITORS.
REMARK 900 RELATED ID: 2CJX RELATED DB: PDB
REMARK 900 EXTENDED SUBSTRATE RECOGNITION IN CASPASE-3 REVEALED BY HIGH
REMARK 900 RESOLUTION X-RAY STRUCTURE ANALYSIS
REMARK 900 RELATED ID: 2CJY RELATED DB: PDB
REMARK 900 EXTENDED SUBSTRATE RECOGNITION IN CASPASE-3 REVEALED BY HIGH
REMARK 900 RESOLUTION X-RAY STRUCTURE ANALYSIS
REMARK 900 RELATED ID: 2CNK RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURES OF CASPASE-3 IN COMPLEX WITH AZA-PEPTIDE EPOXIDE
REMARK 900 INHIBITORS.
REMARK 900 RELATED ID: 2CNL RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURES OF CASPASE-3 IN COMPLEX WITH AZA-PEPTIDE EPOXIDE
REMARK 900 INHIBITORS.
REMARK 900 RELATED ID: 2CNN RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURES OF CASPASE-3 IN COMPLEX WITH AZA-PEPTIDE EPOXIDE
REMARK 900 INHIBITORS.
REMARK 900 RELATED ID: 2CNO RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURES OF CASPASE-3 IN COMPLEX WITH AZA-PEPTIDE EPOXIDE
REMARK 900 INHIBITORS.
REMARK 900 RELATED ID: 2J30 RELATED DB: PDB
REMARK 900 THE ROLE OF LOOP BUNDLE HYDROGEN BONDS IN THE MATURATION AND
REMARK 900 ACTIVITY OF (PRO) CASPASE-3
REMARK 900 RELATED ID: 2J31 RELATED DB: PDB
REMARK 900 THE ROLE OF LOOP BUNDLE HYDROGEN BONDS IN THE MATURATION AND
REMARK 900 ACTIVITY OF(PRO)CASPASE -3
REMARK 900 RELATED ID: 2J32 RELATED DB: PDB
REMARK 900 THE ROLE OF LOOP BUNDLE HYDROGEN BONDS IN THE MATURATION AND
REMARK 900 ACTIVITY OF(PRO)CASPASE -3
REMARK 900 RELATED ID: 2J33 RELATED DB: PDB
REMARK 900 THE ROLE OF LOOP BUNDLE HYDROGEN BONDS IN THE MATURATION AND
REMARK 900 ACTIVITY OF (PRO) CASPASE-3
DBREF 2C2O A 29 175 UNP P42574 CASP3_HUMAN 29 175
DBREF 2C2O B 175 175 PDB 2C2O 2C2O 175 175
DBREF 2C2O B 176 277 UNP P42574 CASP3_HUMAN 176 277
DBREF 2C2O C 1 5 PDB 2C2O 2C2O 1 5
SEQRES 1 A 147 SER GLY ILE SER LEU ASP ASN SER TYR LYS MET ASP TYR
SEQRES 2 A 147 PRO GLU MET GLY LEU CYS ILE ILE ILE ASN ASN LYS ASN
SEQRES 3 A 147 PHE HIS LYS SER THR GLY MET THR SER ARG SER GLY THR
SEQRES 4 A 147 ASP VAL ASP ALA ALA ASN LEU ARG GLU THR PHE ARG ASN
SEQRES 5 A 147 LEU LYS TYR GLU VAL ARG ASN LYS ASN ASP LEU THR ARG
SEQRES 6 A 147 GLU GLU ILE VAL GLU LEU MET ARG ASP VAL SER LYS GLU
SEQRES 7 A 147 ASP HIS SER LYS ARG SER SER PHE VAL CYS VAL LEU LEU
SEQRES 8 A 147 SER HIS GLY GLU GLU GLY ILE ILE PHE GLY THR ASN GLY
SEQRES 9 A 147 PRO VAL ASP LEU LYS LYS ILE THR ASN PHE PHE ARG GLY
SEQRES 10 A 147 ASP ARG CYS ARG SER LEU THR GLY LYS PRO LYS LEU PHE
SEQRES 11 A 147 ILE ILE GLN ALA CYS ARG GLY THR GLU LEU ASP CYS GLY
SEQRES 12 A 147 ILE GLU THR ASP
SEQRES 1 B 103 ALA SER GLY VAL ASP ASP ASP MET ALA CYS HIS LYS ILE
SEQRES 2 B 103 PRO VAL GLU ALA ASP PHE LEU TYR ALA TYR SER THR ALA
SEQRES 3 B 103 PRO GLY TYR TYR SER TRP ARG ASN SER LYS ASP GLY SER
SEQRES 4 B 103 TRP PHE ILE GLN SER LEU CYS ALA MET LEU LYS GLN TYR
SEQRES 5 B 103 ALA ASP LYS LEU GLU PHE MET HIS ILE LEU THR ARG VAL
SEQRES 6 B 103 ASN ARG LYS VAL ALA THR GLU PHE GLU SER PHE SER PHE
SEQRES 7 B 103 ASP ALA THR PHE HIS ALA LYS LYS GLN ILE PRO CYS ILE
SEQRES 8 B 103 VAL SER MET LEU THR LYS GLU LEU TYR PHE TYR HIS
SEQRES 1 C 5 PHQ ASP GLU VAL MX3
HET PHQ C 1 10
HET MX3 C 5 21
HETNAM PHQ BENZYL CHLOROCARBONATE
HETNAM MX3 (1-{4-[BENZYL(METHYL)AMINO]-4-OXOBUTANOYL}HYDRAZINO)
HETNAM 2 MX3 ACETIC ACID
HETSYN MX3 AZA-ASPARTATE-N-BENZYL-N-METHYL-ACRYLAMIDE
FORMUL 3 PHQ C8 H7 CL O2
FORMUL 3 MX3 C14 H19 N3 O4
FORMUL 4 HOH *149(H2 O)
HELIX 1 1 HIS A 56 GLY A 60 5 5
HELIX 2 2 GLY A 66 ASN A 80 1 15
HELIX 3 3 THR A 92 LYS A 105 1 14
HELIX 4 4 LEU A 136 PHE A 142 1 7
HELIX 5 5 CYS A 148 THR A 152 5 5
HELIX 6 6 TRP B 214 ALA B 227 1 14
HELIX 7 7 GLU B 231 PHE B 247 1 17
HELIX 8 8 ASP B 253 HIS B 257 5 5
SHEET 1 AA 6 GLU A 84 ASN A 89 0
SHEET 2 AA 6 GLU A 43 ASN A 51 1 O GLY A 45 N GLU A 84
SHEET 3 AA 6 ARG A 111 LEU A 119 1 N SER A 112 O GLU A 43
SHEET 4 AA 6 LYS A 156 GLN A 161 1 O LEU A 157 N CYS A 116
SHEET 5 AA 6 PHE B 193 TYR B 197 1 O LEU B 194 N PHE A 158
SHEET 6 AA 6 CYS B 264 SER B 267 -1 O CYS B 264 N TYR B 197
SHEET 1 AB 3 GLY A 122 GLU A 123 0
SHEET 2 AB 3 ILE A 126 PHE A 128 -1 O ILE A 126 N GLU A 123
SHEET 3 AB 3 PRO A 133 ASP A 135 -1 O VAL A 134 N ILE A 127
SHEET 1 BA 2 ARG B 207 ASN B 208 0
SHEET 2 BA 2 GLY B 212 SER B 213 -1 O GLY B 212 N ASN B 208
LINK SG CYS A 163 C10 MX3 C 5 1555 1555 1.91
LINK C1 PHQ C 1 N ASP C 2 1555 1555 1.33
LINK C VAL C 4 N MX3 C 5 1555 1555 1.31
SITE 1 AC1 23 ARG A 64 SER A 65 GLU A 84 SER A 120
SITE 2 AC1 23 HIS A 121 GLY A 122 GLU A 123 PHE A 128
SITE 3 AC1 23 GLN A 161 ALA A 162 CYS A 163 THR A 166
SITE 4 AC1 23 ASP B 179 TYR B 204 SER B 205 TRP B 206
SITE 5 AC1 23 ARG B 207 ASN B 208 SER B 209 TRP B 214
SITE 6 AC1 23 SER B 249 PHE B 250 HOH C2087
CRYST1 66.402 83.491 96.356 90.00 90.00 90.00 I 2 2 2 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 0.015060 0.000000 0.000000 0.00000
SCALE2 0.000000 0.011977 0.000000 0.00000
SCALE3 0.000000 0.000000 0.010378 0.00000
(ATOM LINES ARE NOT SHOWN.)
END