HEADER HYDROLASE/HYDROLASE INHIBITOR 17-AUG-06 2J31
TITLE THE ROLE OF LOOP BUNDLE HYDROGEN BONDS IN THE MATURATION AND ACTIVITY
TITLE 2 OF(PRO)CASPASE-3
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: CASPASE-3;
COMPND 3 CHAIN: A;
COMPND 4 FRAGMENT: RESIDUES 29-277;
COMPND 5 SYNONYM: CASP-3, APOPAIN, CYSTEINE PROTEASE CPP32, CPP-32, PROTEIN
COMPND 6 YAMA, SREBP CLEAVAGE ACTIVITY 1, SCA-1, CASPASE-3 SUBUNIT P17,
COMPND 7 CASPASE-3 SUBUNIT P12;
COMPND 8 EC: 3.4.22.56;
COMPND 9 ENGINEERED: YES;
COMPND 10 MUTATION: YES;
COMPND 11 MOL_ID: 2;
COMPND 12 MOLECULE: ACE-ASP-GLU-VAL-ASP-CHLOROMETHYLKETONE INHIBITOR;
COMPND 13 CHAIN: B;
COMPND 14 SYNONYM: AC-DEVD-CMK;
COMPND 15 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 3 ORGANISM_COMMON: HUMAN;
SOURCE 4 ORGANISM_TAXID: 9606;
SOURCE 5 GENE: CASP3, CPP32;
SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE 8 MOL_ID: 2;
SOURCE 9 SYNTHETIC: YES;
SOURCE 10 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT;
SOURCE 11 ORGANISM_TAXID: 32630
KEYWDS CASPASE3 MUTANT E167A, THIOL PROTEASE, HYDROLASE, HYDROLASE-HYDROLASE
KEYWDS 2 INHIBITOR COMPLEX
EXPDTA X-RAY DIFFRACTION
AUTHOR B.FEENEY,C.POP,P.SWARTZ,C.MATTOS,A.C.CLARK
REVDAT 5 08-MAY-19 2J31 1 REMARK LINK
REVDAT 4 21-DEC-16 2J31 1 SOURCE
REVDAT 3 13-JUL-11 2J31 1 VERSN
REVDAT 2 24-FEB-09 2J31 1 VERSN
REVDAT 1 08-NOV-06 2J31 0
JRNL AUTH B.FEENEY,C.POP,P.SWARTZ,C.MATTOS,A.C.CLARK
JRNL TITL ROLE OF LOOP BUNDLE HYDROGEN BONDS IN THE MATURATION AND
JRNL TITL 2 ACTIVITY OF (PRO)CASPASE-3.
JRNL REF BIOCHEMISTRY V. 45 13249 2006
JRNL REFN ISSN 0006-2960
JRNL PMID 17073446
JRNL DOI 10.1021/BI0611964
REMARK 2
REMARK 2 RESOLUTION. 1.50 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) : 1.50
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.67
REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000
REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 694985.300
REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL
REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 93.5
REMARK 3 NUMBER OF REFLECTIONS : 40798
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) : 0.200
REMARK 3 FREE R VALUE : 0.216
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.100
REMARK 3 FREE R VALUE TEST SET COUNT : 4111
REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.003
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) : 1.50
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.59
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 79.70
REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 5143
REMARK 3 BIN R VALUE (WORKING SET) : 0.2840
REMARK 3 BIN FREE R VALUE : 0.2930
REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 9.90
REMARK 3 BIN FREE R VALUE TEST SET COUNT : 566
REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.012
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 1971
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 0
REMARK 3 SOLVENT ATOMS : 204
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 17.70
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.80
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : 3.50000
REMARK 3 B22 (A**2) : 1.90000
REMARK 3 B33 (A**2) : -5.40000
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) : 0.17
REMARK 3 ESD FROM SIGMAA (A) : 0.15
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) : 0.19
REMARK 3 ESD FROM C-V SIGMAA (A) : 0.16
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES.
REMARK 3 BOND LENGTHS (A) : 0.005
REMARK 3 BOND ANGLES (DEGREES) : 1.300
REMARK 3 DIHEDRAL ANGLES (DEGREES) : 24.30
REMARK 3 IMPROPER ANGLES (DEGREES) : 1.000
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) : 1.100 ; 1.500
REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.700 ; 2.000
REMARK 3 SIDE-CHAIN BOND (A**2) : 2.100 ; 2.000
REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.160 ; 2.500
REMARK 3
REMARK 3 BULK SOLVENT MODELING.
REMARK 3 METHOD USED : FLAT MODEL
REMARK 3 KSOL : 0.40
REMARK 3 BSOL : 39.58
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.PARAM
REMARK 3 PARAMETER FILE 2 : WATER.PARAM
REMARK 3 PARAMETER FILE 3 : ACE.PARAM
REMARK 3 PARAMETER FILE 4 : ASK.PARAM
REMARK 3 PARAMETER FILE 5 : NULL
REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP
REMARK 3 TOPOLOGY FILE 2 : WATER.TOP
REMARK 3 TOPOLOGY FILE 3 : ACE.TOP
REMARK 3 TOPOLOGY FILE 4 : ASK.TOP
REMARK 3 TOPOLOGY FILE 5 : NULL
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 2J31 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 17-AUG-06.
REMARK 100 THE DEPOSITION ID IS D_1290029703.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : NULL
REMARK 200 TEMPERATURE (KELVIN) : 100.0
REMARK 200 PH : 8.50
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : APS
REMARK 200 BEAMLINE : 22-ID
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 1.0
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000
REMARK 200 DATA SCALING SOFTWARE : SCALEPACK
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 49333
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500
REMARK 200 RESOLUTION RANGE LOW (A) : 50.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 92.2
REMARK 200 DATA REDUNDANCY : 5.100
REMARK 200 R MERGE (I) : 0.09000
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 34.6000
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 (%) : 90.5
REMARK 200 DATA REDUNDANCY IN SHELL : 3.00
REMARK 200 R MERGE FOR SHELL (I) : 0.43000
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.500
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
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 (%): 44.02
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.21
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 8 MG/ML PRO-CASPASE3 IN 10 MM TRIS-
REMARK 280 HCL, PH 8.5, 1 MM DTT. THE PROTEIN WAS CONCENTRATED TO 10 MG/ML
REMARK 280 USING AMICON ULTRAFREE CENTRIFUGAL FILTER DEVICES, AND INHIBITOR,
REMARK 280 AC-DEVD-CMK RECONSTITUTED IN DMSO, WAS THEN ADDED AT 5:1 WT:WT,
REMARK 280 INHIBITOR TO PEPTIDE. THE PROTEIN WAS DILUTED TO A CONCENTRATION
REMARK 280 OF 8 MG/ML BY ADDING 10 MM TRIS-HCL, PH 8.5, CONCENTRATED DTT
REMARK 280 AND CONCENTRATED NAN3 SO THAT THE FINAL BUFFER WAS 10 MM TRIS-
REMARK 280 HCL, PH 8.5, 10 MM DTT, 3 MM NAN3. 2 UL OF CONCENTRATED PROTEIN
REMARK 280 WAS MIXED 1:1 WITH WELL BUFFER THAT CONTAINED 100 MM SODIUM
REMARK 280 CITRATE, PH 5, 3 MM NAN3, 10 MM DTT AND 17% PEG 6000 W/V.
REMARK 280 SOLUTIONS WERE INCUBATED AT 18 DEG C USING THE HANGING DROP
REMARK 280 METHOD. CRYSTALS GREW WITHIN THREE DAYS FOR WILD-TYPE CASPASE-3
REMARK 280 AND WITHIN TWO WEEKS FOR THE MUTANTS. THE IDEAL FREEZING
REMARK 280 CONDITIONS WERE FOUND TO BE WITH 80% MOTHER LIQUOR AND 20% PEG
REMARK 280 400., PH 8.50, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K
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 33.66600
REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 41.96250
REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 47.75200
REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 33.66600
REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 41.96250
REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 47.75200
REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 33.66600
REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 41.96250
REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 47.75200
REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 33.66600
REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 41.96250
REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 47.75200
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: OCTAMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: OCTAMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 16550 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 35560 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -55.0 KCAL/MOL
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 67.33200
REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 83.92500
REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000
REMARK 350 BIOMT1 3 -1.000000 0.000000 0.000000 67.33200
REMARK 350 BIOMT2 3 0.000000 1.000000 0.000000 0.00000
REMARK 350 BIOMT3 3 0.000000 0.000000 -1.000000 95.50400
REMARK 350 BIOMT1 4 1.000000 0.000000 0.000000 0.00000
REMARK 350 BIOMT2 4 0.000000 -1.000000 0.000000 83.92500
REMARK 350 BIOMT3 4 0.000000 0.000000 -1.000000 95.50400
REMARK 375
REMARK 375 SPECIAL POSITION
REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS
REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL
REMARK 375 POSITIONS.
REMARK 375
REMARK 375 ATOM RES CSSEQI
REMARK 375 HOH A2024 LIES ON A SPECIAL POSITION.
REMARK 375 HOH A2093 LIES ON A SPECIAL POSITION.
REMARK 375 HOH A2162 LIES ON A SPECIAL POSITION.
REMARK 400
REMARK 400 COMPOUND
REMARK 400
REMARK 400 THE AC-ASP-GLU-VAL-ASP-CMK IS PEPTIDE-LIKE, A MEMBER OF INHIBITOR
REMARK 400 CLASS.
REMARK 400
REMARK 400 GROUP: 1
REMARK 400 NAME: AC-ASP-GLU-VAL-ASP-CMK
REMARK 400 CHAIN: B
REMARK 400 COMPONENT_1: PEPTIDE LIKE POLYMER
REMARK 400 DESCRIPTION: NULL
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 ASP A 175
REMARK 465 SER A 176
REMARK 465 GLY A 177
REMARK 465 VAL A 178
REMARK 465 ASP A 179
REMARK 465 ASP A 180
REMARK 465 ASP A 181
REMARK 465 MET A 182
REMARK 465 ALA A 183
REMARK 465 CYS A 184
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT
REMARK 500
REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT.
REMARK 500
REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE
REMARK 500 NE2 HIS A 278 O HOH A 2200 2.03
REMARK 500 O HOH A 2131 O HOH A 2150 2.15
REMARK 500 O HOH A 2111 O HOH A 2113 2.16
REMARK 500
REMARK 500 REMARK: NULL
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 O HOH A 2047 O HOH A 2097 2655 2.13
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 SER A 120 -174.79 -172.69
REMARK 500 LYS A 229 -45.44 -135.82
REMARK 500
REMARK 500 REMARK: NULL
REMARK 525
REMARK 525 SOLVENT
REMARK 525
REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT
REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST
REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT
REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE
REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER;
REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE
REMARK 525 NUMBER; I=INSERTION CODE):
REMARK 525
REMARK 525 M RES CSSEQI
REMARK 525 HOH A2017 DISTANCE = 6.28 ANGSTROMS
REMARK 525 HOH A2022 DISTANCE = 7.20 ANGSTROMS
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR CHAIN B OF ACE-ASP-GLU-VAL-ASP
REMARK 800 -CHLOROMETHYLKETONE INHIBITOR
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: 2C2O 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. RELATED ENTRIES
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)
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 2J31 A 29 277 UNP P42574 CASP3_HUMAN 29 277
DBREF 2J31 B 1 6 PDB 2J31 2J31 1 6
SEQADV 2J31 ALA A 167 UNP P42574 GLU 167 ENGINEERED MUTATION
SEQADV 2J31 HIS A 278 UNP P42574 EXPRESSION TAG
SEQRES 1 A 250 SER GLY ILE SER LEU ASP ASN SER TYR LYS MET ASP TYR
SEQRES 2 A 250 PRO GLU MET GLY LEU CYS ILE ILE ILE ASN ASN LYS ASN
SEQRES 3 A 250 PHE HIS LYS SER THR GLY MET THR SER ARG SER GLY THR
SEQRES 4 A 250 ASP VAL ASP ALA ALA ASN LEU ARG GLU THR PHE ARG ASN
SEQRES 5 A 250 LEU LYS TYR GLU VAL ARG ASN LYS ASN ASP LEU THR ARG
SEQRES 6 A 250 GLU GLU ILE VAL GLU LEU MET ARG ASP VAL SER LYS GLU
SEQRES 7 A 250 ASP HIS SER LYS ARG SER SER PHE VAL CYS VAL LEU LEU
SEQRES 8 A 250 SER HIS GLY GLU GLU GLY ILE ILE PHE GLY THR ASN GLY
SEQRES 9 A 250 PRO VAL ASP LEU LYS LYS ILE THR ASN PHE PHE ARG GLY
SEQRES 10 A 250 ASP ARG CYS ARG SER LEU THR GLY LYS PRO LYS LEU PHE
SEQRES 11 A 250 ILE ILE GLN ALA CYS ARG GLY THR ALA LEU ASP CYS GLY
SEQRES 12 A 250 ILE GLU THR ASP SER GLY VAL ASP ASP ASP MET ALA CYS
SEQRES 13 A 250 HIS LYS ILE PRO VAL GLU ALA ASP PHE LEU TYR ALA TYR
SEQRES 14 A 250 SER THR ALA PRO GLY TYR TYR SER TRP ARG ASN SER LYS
SEQRES 15 A 250 ASP GLY SER TRP PHE ILE GLN SER LEU CYS ALA MET LEU
SEQRES 16 A 250 LYS GLN TYR ALA ASP LYS LEU GLU PHE MET HIS ILE LEU
SEQRES 17 A 250 THR ARG VAL ASN ARG LYS VAL ALA THR GLU PHE GLU SER
SEQRES 18 A 250 PHE SER PHE ASP ALA THR PHE HIS ALA LYS LYS GLN ILE
SEQRES 19 A 250 PRO CYS ILE VAL SER MET LEU THR LYS GLU LEU TYR PHE
SEQRES 20 A 250 TYR HIS HIS
SEQRES 1 B 6 ACE ASP GLU VAL ASP 0QE
HET ACE B 1 3
HET 0QE B 6 1
HETNAM ACE ACETYL GROUP
HETNAM 0QE CHLOROMETHANE
HETSYN 0QE CHLORO METHYL GROUP
FORMUL 2 ACE C2 H4 O
FORMUL 2 0QE C H3 CL
FORMUL 3 HOH *204(H2 O)
HELIX 1 1 HIS A 56 GLY A 60 5 5
HELIX 2 2 GLY A 66 LEU A 81 1 16
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 A 214 ALA A 227 1 14
HELIX 7 7 GLU A 231 PHE A 247 1 17
HELIX 8 8 ASP A 253 HIS A 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 A 193 TYR A 197 1 O LEU A 194 N PHE A 158
SHEET 6 AA 6 CYS A 264 SER A 267 -1 O CYS A 264 N TYR A 197
SHEET 1 AB 3 GLY A 122 GLU A 123 0
SHEET 2 AB 3 ILE A 126 GLY A 129 -1 O ILE A 126 N GLU A 123
SHEET 3 AB 3 GLY A 132 ASP A 135 -1 O GLY A 132 N GLY A 129
SHEET 1 AC 3 GLY A 212 SER A 213 0
SHEET 2 AC 3 TRP A 206 ASN A 208 -1 O ASN A 208 N GLY A 212
SHEET 3 AC 3 GLU B 3 VAL B 4 -1 O GLU B 3 N ARG A 207
LINK C ACE B 1 N ASP B 2 1555 1555 1.33
LINK C ASP B 5 C1 0QE B 6 1555 1555 1.53
SITE 1 AC1 21 SER A 58 ARG A 64 HIS A 121 GLY A 122
SITE 2 AC1 21 GLN A 161 CYS A 163 TYR A 204 SER A 205
SITE 3 AC1 21 TRP A 206 ARG A 207 ASN A 208 SER A 209
SITE 4 AC1 21 TRP A 214 SER A 249 PHE A 250 HOH A2031
SITE 5 AC1 21 HOH A2179 HOH B2001 HOH B2002 HOH B2003
SITE 6 AC1 21 HOH B2004
CRYST1 67.332 83.925 95.504 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 0.014852 0.000000 0.000000 0.00000
SCALE2 0.000000 0.011915 0.000000 0.00000
SCALE3 0.000000 0.000000 0.010471 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
