HEADER HYDROLASE, APOPTOSIS 10-JUN-08 3DEI TITLE CRYSTAL STRUCTURES OF CASPASE-3 WITH BOUND ISOQUINOLINE-1,3,4-TRIONE TITLE 2 DERIVATIVE INHIBITORS COMPND MOL_ID: 1; COMPND 2 MOLECULE: CASPASE-3; COMPND 3 CHAIN: A, B, C, D; COMPND 4 SYNONYM: CASP-3, APOPAIN, CYSTEINE PROTEASE CPP32, YAMA PROTEIN, CPP- COMPND 5 32, SREBP CLEAVAGE ACTIVITY 1, SCA-1, CASPASE-3 SUBUNIT P17, CASPASE- COMPND 6 3 SUBUNIT P12; COMPND 7 EC: 3.4.22.56; COMPND 8 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 BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET32B KEYWDS CASPASE-3, ISOQUINOLINE-1, 3, 4-TRIONE DERIVATIVES, INACTIVATION, KEYWDS 2 PROTEIN-INHIBITOR COMPLEX, APOPTOSIS, CYTOPLASM, HYDROLASE, KEYWDS 3 PHOSPHOPROTEIN, POLYMORPHISM, PROTEASE, S-NITROSYLATION, THIOL KEYWDS 4 PROTEASE, ZYMOGEN EXPDTA X-RAY DIFFRACTION AUTHOR J.WU,J.DU,J.LI,J.DING REVDAT 5 01-NOV-23 3DEI 1 REMARK LINK REVDAT 4 25-OCT-17 3DEI 1 REMARK REVDAT 3 24-FEB-09 3DEI 1 VERSN REVDAT 2 04-NOV-08 3DEI 1 JRNL REVDAT 1 02-SEP-08 3DEI 0 JRNL AUTH J.-Q.DU,J.WU,H.-J.ZHANG,Y.-H.ZHANG,B.-Y.QIU,F.WU,Y.-H.CHEN, JRNL AUTH 2 J.-Y.LI,F.-J.NAN,J.-P.DING,J.LI JRNL TITL ISOQUINOLINE-1,3,4-TRIONE DERIVATIVES INACTIVATE CASPASE-3 JRNL TITL 2 BY GENERATION OF REACTIVE OXYGEN SPECIES JRNL REF J.BIOL.CHEM. V. 283 30205 2008 JRNL REFN ISSN 0021-9258 JRNL PMID 18768468 JRNL DOI 10.1074/JBC.M803347200 REMARK 2 REMARK 2 RESOLUTION. 2.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.1.24 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.13 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.1 REMARK 3 NUMBER OF REFLECTIONS : 27133 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 + TEST SET) : 0.215 REMARK 3 R VALUE (WORKING SET) : 0.211 REMARK 3 FREE R VALUE : 0.291 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1366 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.87 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1789 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.3150 REMARK 3 BIN FREE R VALUE SET COUNT : 105 REMARK 3 BIN FREE R VALUE : 0.4220 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 7571 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 27 REMARK 3 SOLVENT ATOMS : 74 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 72.77 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.29000 REMARK 3 B22 (A**2) : 0.30000 REMARK 3 B33 (A**2) : -0.02000 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 OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.461 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.329 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 16.494 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.935 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.888 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 7758 ; 0.012 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 10433 ; 1.421 ; 1.954 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 925 ; 5.614 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 1121 ; 0.096 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5827 ; 0.004 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 3618 ; 0.241 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 315 ; 0.165 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 23 ; 0.178 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 2 ; 0.213 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 4633 ; 1.814 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 7476 ; 3.585 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 3125 ; 4.034 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2957 ; 6.998 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 7758 ; 2.125 ; 2.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 74 ; 2.190 ; 2.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 7599 ; 1.224 ; 2.000 REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3DEI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 12-JUN-08. REMARK 100 THE DEPOSITION ID IS D_1000047938. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-JUN-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.4 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : BL-17A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 270 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO, HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK, HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 27196 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.800 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.3 REMARK 200 DATA REDUNDANCY : 5.000 REMARK 200 R MERGE (I) : 0.12800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.90 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.7 REMARK 200 DATA REDUNDANCY IN SHELL : 4.70 REMARK 200 R MERGE FOR SHELL (I) : 0.53000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL 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 1GFW REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.48 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.48 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 4-6% POLYETHYLENE GLYCOL 6000, 0.1M REMARK 280 HEPES PH 7.6, 20MM L-CYSTEINE, 5% GLYCEROL, PH 7.4, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 277K 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 32.76050 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 90.26400 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 47.99200 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 90.26400 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 32.76050 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 47.99200 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, 3 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4080 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18690 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -18.0 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 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4120 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19150 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -20.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D 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: 3 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 10190 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 35850 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -45.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D 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 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 29 REMARK 465 GLY A 30 REMARK 465 ILE A 31 REMARK 465 SER A 32 REMARK 465 LEU A 33 REMARK 465 THR A 174 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 465 HIS A 185 REMARK 465 SER B 29 REMARK 465 GLY B 30 REMARK 465 ILE B 31 REMARK 465 SER B 32 REMARK 465 THR B 174 REMARK 465 ASP B 175 REMARK 465 SER B 176 REMARK 465 GLY B 177 REMARK 465 VAL B 178 REMARK 465 ASP B 179 REMARK 465 ASP B 180 REMARK 465 ASP B 181 REMARK 465 MET B 182 REMARK 465 ALA B 183 REMARK 465 CYS B 184 REMARK 465 HIS B 185 REMARK 465 SER C 29 REMARK 465 GLY C 30 REMARK 465 ILE C 31 REMARK 465 SER C 32 REMARK 465 THR C 174 REMARK 465 ASP C 175 REMARK 465 SER C 176 REMARK 465 GLY C 177 REMARK 465 VAL C 178 REMARK 465 ASP C 179 REMARK 465 ASP C 180 REMARK 465 ASP C 181 REMARK 465 MET C 182 REMARK 465 ALA C 183 REMARK 465 CYS C 184 REMARK 465 SER D 29 REMARK 465 GLY D 30 REMARK 465 ILE D 31 REMARK 465 THR D 174 REMARK 465 ASP D 175 REMARK 465 SER D 176 REMARK 465 GLY D 177 REMARK 465 VAL D 178 REMARK 465 ASP D 179 REMARK 465 ASP D 180 REMARK 465 ASP D 181 REMARK 465 MET D 182 REMARK 465 ALA D 183 REMARK 465 CYS D 184 REMARK 465 HIS D 277 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 ASP A 34 CB - CG - OD2 ANGL. DEV. = 5.7 DEGREES REMARK 500 ASP A 40 CB - CG - OD2 ANGL. DEV. = 5.4 DEGREES REMARK 500 ASP A 102 CB - CG - OD2 ANGL. DEV. = 6.7 DEGREES REMARK 500 ASP A 135 CB - CG - OD2 ANGL. DEV. = 5.5 DEGREES REMARK 500 ASP A 190 CB - CG - OD2 ANGL. DEV. = 6.1 DEGREES REMARK 500 ASP B 90 CB - CG - OD2 ANGL. DEV. = 6.0 DEGREES REMARK 500 ASP B 190 CB - CG - OD2 ANGL. DEV. = 6.4 DEGREES REMARK 500 ASP C 135 CB - CG - OD2 ANGL. DEV. = 5.5 DEGREES REMARK 500 ASP C 190 CB - CG - OD2 ANGL. DEV. = 5.6 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 CYS A 148 68.75 -117.75 REMARK 500 ALA A 162 144.26 -178.75 REMARK 500 TYR A 226 -16.25 -143.15 REMARK 500 ALA A 227 -19.84 -44.17 REMARK 500 PHE A 275 5.39 -69.66 REMARK 500 ASP B 40 45.28 -94.92 REMARK 500 LYS B 82 25.19 85.66 REMARK 500 HIS B 108 35.28 -91.79 REMARK 500 SER B 120 -178.54 -175.40 REMARK 500 LYS B 229 -73.72 -122.67 REMARK 500 MET B 268 40.23 -106.92 REMARK 500 THR C 59 -33.86 -37.90 REMARK 500 LYS C 82 40.25 82.88 REMARK 500 ASP C 90 74.37 39.75 REMARK 500 CYS C 148 66.75 -159.14 REMARK 500 LYS C 229 -46.79 -136.42 REMARK 500 ASP D 34 34.23 -171.65 REMARK 500 ASN D 73 -39.91 -39.04 REMARK 500 LEU D 74 -70.75 -74.59 REMARK 500 ARG D 75 -45.83 -25.25 REMARK 500 GLU D 76 -74.42 -66.87 REMARK 500 LYS D 82 32.68 94.93 REMARK 500 ASP D 90 58.63 33.17 REMARK 500 GLU D 106 -178.17 -56.87 REMARK 500 SER D 120 -175.71 -172.68 REMARK 500 GLU D 123 -158.11 -113.08 REMARK 500 GLU D 167 150.66 -42.13 REMARK 500 ALA D 227 -15.98 -45.79 REMARK 500 LYS D 229 -59.35 -141.83 REMARK 500 GLU D 248 137.86 -178.92 REMARK 500 ALA D 258 30.09 70.87 REMARK 500 REMARK 500 REMARK: NULL REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 THE INHIBITOR WAS SYNTHESIZED AT CHINESE NATIONAL CENTER REMARK 600 FOR DRUG SCREENING REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE RXB C 300 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3DEH RELATED DB: PDB REMARK 900 CASPASE-3 COMPLEXED WITH AN INHIBITOR(RXA) REMARK 900 RELATED ID: 3DEJ RELATED DB: PDB REMARK 900 CASPASE-3 COMPLEXED WITH AN INHIBITOR(RXC) REMARK 900 RELATED ID: 3DEK RELATED DB: PDB REMARK 900 CASPASE-3 COMPLEXED WITH AN INHIBITOR(RXD) REMARK 999 REMARK 999 SEQUENCE REMARK 999 190TH RESIDUE IN ALL CHAINS IS ASP AND IS A NATURAL REMARK 999 VARIANT FOR CASP3_HUMAN. DBREF 3DEI A 29 277 UNP P42574 CASP3_HUMAN 29 277 DBREF 3DEI B 29 277 UNP P42574 CASP3_HUMAN 29 277 DBREF 3DEI C 29 277 UNP P42574 CASP3_HUMAN 29 277 DBREF 3DEI D 29 277 UNP P42574 CASP3_HUMAN 29 277 SEQADV 3DEI ASP A 190 UNP P42574 GLU 190 SEE REMARK 999 SEQADV 3DEI ASP B 190 UNP P42574 GLU 190 SEE REMARK 999 SEQADV 3DEI ASP C 190 UNP P42574 GLU 190 SEE REMARK 999 SEQADV 3DEI ASP D 190 UNP P42574 GLU 190 SEE REMARK 999 SEQRES 1 A 249 SER GLY ILE SER LEU ASP ASN SER TYR LYS MET ASP TYR SEQRES 2 A 249 PRO GLU MET GLY LEU CYS ILE ILE ILE ASN ASN LYS ASN SEQRES 3 A 249 PHE HIS LYS SER THR GLY MET THR SER ARG SER GLY THR SEQRES 4 A 249 ASP VAL ASP ALA ALA ASN LEU ARG GLU THR PHE ARG ASN SEQRES 5 A 249 LEU LYS TYR GLU VAL ARG ASN LYS ASN ASP LEU THR ARG SEQRES 6 A 249 GLU GLU ILE VAL GLU LEU MET ARG ASP VAL SER LYS GLU SEQRES 7 A 249 ASP HIS SER LYS ARG SER SER PHE VAL CYS VAL LEU LEU SEQRES 8 A 249 SER HIS GLY GLU GLU GLY ILE ILE PHE GLY THR ASN GLY SEQRES 9 A 249 PRO VAL ASP LEU LYS LYS ILE THR ASN PHE PHE ARG GLY SEQRES 10 A 249 ASP ARG CYS ARG SER LEU THR GLY LYS PRO LYS LEU PHE SEQRES 11 A 249 ILE ILE GLN ALA OCS ARG GLY THR GLU LEU ASP CYS GLY SEQRES 12 A 249 ILE GLU THR ASP SER GLY VAL ASP ASP ASP MET ALA CYS SEQRES 13 A 249 HIS LYS ILE PRO VAL ASP ALA ASP PHE LEU TYR ALA TYR SEQRES 14 A 249 SER THR ALA PRO GLY TYR TYR SER TRP ARG ASN SER LYS SEQRES 15 A 249 ASP GLY SER TRP PHE ILE GLN SER LEU CYS ALA MET LEU SEQRES 16 A 249 LYS GLN TYR ALA ASP LYS LEU GLU PHE MET HIS ILE LEU SEQRES 17 A 249 THR ARG VAL ASN ARG LYS VAL ALA THR GLU PHE GLU SER SEQRES 18 A 249 PHE SER PHE ASP ALA THR PHE HIS ALA LYS LYS GLN ILE SEQRES 19 A 249 PRO CYS ILE VAL SER MET LEU THR LYS GLU LEU TYR PHE SEQRES 20 A 249 TYR HIS SEQRES 1 B 249 SER GLY ILE SER LEU ASP ASN SER TYR LYS MET ASP TYR SEQRES 2 B 249 PRO GLU MET GLY LEU CYS ILE ILE ILE ASN ASN LYS ASN SEQRES 3 B 249 PHE HIS LYS SER THR GLY MET THR SER ARG SER GLY THR SEQRES 4 B 249 ASP VAL ASP ALA ALA ASN LEU ARG GLU THR PHE ARG ASN SEQRES 5 B 249 LEU LYS TYR GLU VAL ARG ASN LYS ASN ASP LEU THR ARG SEQRES 6 B 249 GLU GLU ILE VAL GLU LEU MET ARG ASP VAL SER LYS GLU SEQRES 7 B 249 ASP HIS SER LYS ARG SER SER PHE VAL CYS VAL LEU LEU SEQRES 8 B 249 SER HIS GLY GLU GLU GLY ILE ILE PHE GLY THR ASN GLY SEQRES 9 B 249 PRO VAL ASP LEU LYS LYS ILE THR ASN PHE PHE ARG GLY SEQRES 10 B 249 ASP ARG CYS ARG SER LEU THR GLY LYS PRO LYS LEU PHE SEQRES 11 B 249 ILE ILE GLN ALA OCS ARG GLY THR GLU LEU ASP CYS GLY SEQRES 12 B 249 ILE GLU THR ASP SER GLY VAL ASP ASP ASP MET ALA CYS SEQRES 13 B 249 HIS LYS ILE PRO VAL ASP ALA ASP PHE LEU TYR ALA TYR SEQRES 14 B 249 SER THR ALA PRO GLY TYR TYR SER TRP ARG ASN SER LYS SEQRES 15 B 249 ASP GLY SER TRP PHE ILE GLN SER LEU CYS ALA MET LEU SEQRES 16 B 249 LYS GLN TYR ALA ASP LYS LEU GLU PHE MET HIS ILE LEU SEQRES 17 B 249 THR ARG VAL ASN ARG LYS VAL ALA THR GLU PHE GLU SER SEQRES 18 B 249 PHE SER PHE ASP ALA THR PHE HIS ALA LYS LYS GLN ILE SEQRES 19 B 249 PRO CYS ILE VAL SER MET LEU THR LYS GLU LEU TYR PHE SEQRES 20 B 249 TYR HIS SEQRES 1 C 249 SER GLY ILE SER LEU ASP ASN SER TYR LYS MET ASP TYR SEQRES 2 C 249 PRO GLU MET GLY LEU CYS ILE ILE ILE ASN ASN LYS ASN SEQRES 3 C 249 PHE HIS LYS SER THR GLY MET THR SER ARG SER GLY THR SEQRES 4 C 249 ASP VAL ASP ALA ALA ASN LEU ARG GLU THR PHE ARG ASN SEQRES 5 C 249 LEU LYS TYR GLU VAL ARG ASN LYS ASN ASP LEU THR ARG SEQRES 6 C 249 GLU GLU ILE VAL GLU LEU MET ARG ASP VAL SER LYS GLU SEQRES 7 C 249 ASP HIS SER LYS ARG SER SER PHE VAL CYS VAL LEU LEU SEQRES 8 C 249 SER HIS GLY GLU GLU GLY ILE ILE PHE GLY THR ASN GLY SEQRES 9 C 249 PRO VAL ASP LEU LYS LYS ILE THR ASN PHE PHE ARG GLY SEQRES 10 C 249 ASP ARG CYS ARG SER LEU THR GLY LYS PRO LYS LEU PHE SEQRES 11 C 249 ILE ILE GLN ALA OCS ARG GLY THR GLU LEU ASP CYS GLY SEQRES 12 C 249 ILE GLU THR ASP SER GLY VAL ASP ASP ASP MET ALA CYS SEQRES 13 C 249 HIS LYS ILE PRO VAL ASP ALA ASP PHE LEU TYR ALA TYR SEQRES 14 C 249 SER THR ALA PRO GLY TYR TYR SER TRP ARG ASN SER LYS SEQRES 15 C 249 ASP GLY SER TRP PHE ILE GLN SER LEU CYS ALA MET LEU SEQRES 16 C 249 LYS GLN TYR ALA ASP LYS LEU GLU PHE MET HIS ILE LEU SEQRES 17 C 249 THR ARG VAL ASN ARG LYS VAL ALA THR GLU PHE GLU SER SEQRES 18 C 249 PHE SER PHE ASP ALA THR PHE HIS ALA LYS LYS GLN ILE SEQRES 19 C 249 PRO CYS ILE VAL SER MET LEU THR LYS GLU LEU TYR PHE SEQRES 20 C 249 TYR HIS SEQRES 1 D 249 SER GLY ILE SER LEU ASP ASN SER TYR LYS MET ASP TYR SEQRES 2 D 249 PRO GLU MET GLY LEU CYS ILE ILE ILE ASN ASN LYS ASN SEQRES 3 D 249 PHE HIS LYS SER THR GLY MET THR SER ARG SER GLY THR SEQRES 4 D 249 ASP VAL ASP ALA ALA ASN LEU ARG GLU THR PHE ARG ASN SEQRES 5 D 249 LEU LYS TYR GLU VAL ARG ASN LYS ASN ASP LEU THR ARG SEQRES 6 D 249 GLU GLU ILE VAL GLU LEU MET ARG ASP VAL SER LYS GLU SEQRES 7 D 249 ASP HIS SER LYS ARG SER SER PHE VAL CYS VAL LEU LEU SEQRES 8 D 249 SER HIS GLY GLU GLU GLY ILE ILE PHE GLY THR ASN GLY SEQRES 9 D 249 PRO VAL ASP LEU LYS LYS ILE THR ASN PHE PHE ARG GLY SEQRES 10 D 249 ASP ARG CYS ARG SER LEU THR GLY LYS PRO LYS LEU PHE SEQRES 11 D 249 ILE ILE GLN ALA OCS ARG GLY THR GLU LEU ASP CYS GLY SEQRES 12 D 249 ILE GLU THR ASP SER GLY VAL ASP ASP ASP MET ALA CYS SEQRES 13 D 249 HIS LYS ILE PRO VAL ASP ALA ASP PHE LEU TYR ALA TYR SEQRES 14 D 249 SER THR ALA PRO GLY TYR TYR SER TRP ARG ASN SER LYS SEQRES 15 D 249 ASP GLY SER TRP PHE ILE GLN SER LEU CYS ALA MET LEU SEQRES 16 D 249 LYS GLN TYR ALA ASP LYS LEU GLU PHE MET HIS ILE LEU SEQRES 17 D 249 THR ARG VAL ASN ARG LYS VAL ALA THR GLU PHE GLU SER SEQRES 18 D 249 PHE SER PHE ASP ALA THR PHE HIS ALA LYS LYS GLN ILE SEQRES 19 D 249 PRO CYS ILE VAL SER MET LEU THR LYS GLU LEU TYR PHE SEQRES 20 D 249 TYR HIS MODRES 3DEI OCS A 163 CYS CYSTEINESULFONIC ACID MODRES 3DEI OCS B 163 CYS CYSTEINESULFONIC ACID MODRES 3DEI OCS C 163 CYS CYSTEINESULFONIC ACID MODRES 3DEI OCS D 163 CYS CYSTEINESULFONIC ACID HET OCS A 163 9 HET OCS B 163 9 HET OCS C 163 9 HET OCS D 163 9 HET RXB C 300 27 HETNAM OCS CYSTEINESULFONIC ACID HETNAM RXB (1S)-2-OXO-1-PHENYL-2-[(1,3,4-TRIOXO-1,2,3,4- HETNAM 2 RXB TETRAHYDROISOQUINOLIN-5-YL)AMINO]ETHYL ACETATE FORMUL 1 OCS 4(C3 H7 N O5 S) FORMUL 5 RXB C19 H14 N2 O6 FORMUL 6 HOH *74(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 SER A 104 1 13 HELIX 4 4 LEU A 136 ASN A 141 1 6 HELIX 5 5 PHE A 142 ARG A 144 5 3 HELIX 6 6 CYS A 148 THR A 152 5 5 HELIX 7 7 SER A 213 ALA A 227 1 15 HELIX 8 8 GLU A 231 PHE A 247 1 17 HELIX 9 9 ASP A 253 HIS A 257 5 5 HELIX 10 10 GLY B 66 LEU B 81 1 16 HELIX 11 11 THR B 92 GLU B 106 1 15 HELIX 12 12 LEU B 136 PHE B 142 1 7 HELIX 13 13 CYS B 148 THR B 152 5 5 HELIX 14 14 TRP B 214 ALA B 227 1 14 HELIX 15 15 GLU B 231 PHE B 247 1 17 HELIX 16 16 GLY C 66 LEU C 81 1 16 HELIX 17 17 THR C 92 GLU C 106 1 15 HELIX 18 18 LEU C 136 ASN C 141 1 6 HELIX 19 19 PHE C 142 ARG C 144 5 3 HELIX 20 20 TRP C 214 ALA C 227 1 14 HELIX 21 21 GLU C 231 PHE C 247 1 17 HELIX 22 22 ASP C 253 HIS C 257 5 5 HELIX 23 23 GLY D 66 ASN D 80 1 15 HELIX 24 24 THR D 92 SER D 104 1 13 HELIX 25 25 ASP D 107 ARG D 111 5 5 HELIX 26 26 LEU D 136 PHE D 142 1 7 HELIX 27 27 CYS D 148 THR D 152 5 5 HELIX 28 28 SER D 213 ALA D 227 1 15 HELIX 29 29 GLU D 231 GLU D 246 1 16 SHEET 1 A12 GLU A 84 ASN A 89 0 SHEET 2 A12 LEU A 46 ASN A 51 1 N CYS A 47 O ARG A 86 SHEET 3 A12 PHE A 114 LEU A 119 1 O VAL A 117 N ILE A 50 SHEET 4 A12 LYS A 156 GLN A 161 1 O LEU A 157 N PHE A 114 SHEET 5 A12 PHE A 193 TYR A 197 1 O ALA A 196 N PHE A 158 SHEET 6 A12 CYS A 264 SER A 267 -1 O VAL A 266 N TYR A 195 SHEET 7 A12 CYS B 264 MET B 268 -1 O SER B 267 N ILE A 265 SHEET 8 A12 PHE B 193 TYR B 197 -1 N TYR B 195 O VAL B 266 SHEET 9 A12 LYS B 156 GLN B 161 1 N PHE B 158 O ALA B 196 SHEET 10 A12 PHE B 114 LEU B 119 1 N PHE B 114 O LEU B 157 SHEET 11 A12 LEU B 46 ASN B 51 1 N ILE B 50 O VAL B 117 SHEET 12 A12 GLU B 84 ASN B 89 1 O LYS B 88 N ASN B 51 SHEET 1 B 3 GLY A 122 GLU A 123 0 SHEET 2 B 3 ILE A 126 PHE A 128 -1 O ILE A 126 N GLU A 123 SHEET 3 B 3 PRO A 133 ASP A 135 -1 O VAL A 134 N ILE A 127 SHEET 1 C 3 GLY B 122 GLU B 123 0 SHEET 2 C 3 ILE B 126 PHE B 128 -1 O ILE B 126 N GLU B 123 SHEET 3 C 3 PRO B 133 ASP B 135 -1 O VAL B 134 N ILE B 127 SHEET 1 D 2 GLY B 165 GLU B 167 0 SHEET 2 D 2 GLY B 202 TYR B 203 1 O GLY B 202 N GLU B 167 SHEET 1 E 2 ARG B 207 ASN B 208 0 SHEET 2 E 2 GLY B 212 SER B 213 -1 O GLY B 212 N ASN B 208 SHEET 1 F12 GLU C 84 ASN C 89 0 SHEET 2 F12 LEU C 46 ASN C 51 1 N ASN C 51 O LYS C 88 SHEET 3 F12 PHE C 114 LEU C 119 1 O LEU C 119 N ILE C 50 SHEET 4 F12 LYS C 156 GLN C 161 1 O LEU C 157 N PHE C 114 SHEET 5 F12 PHE C 193 TYR C 197 1 O ALA C 196 N ILE C 160 SHEET 6 F12 CYS C 264 MET C 268 -1 O VAL C 266 N TYR C 195 SHEET 7 F12 CYS D 264 MET D 268 -1 O ILE D 265 N SER C 267 SHEET 8 F12 PHE D 193 TYR D 197 -1 N PHE D 193 O MET D 268 SHEET 9 F12 LYS D 156 GLN D 161 1 N PHE D 158 O LEU D 194 SHEET 10 F12 PHE D 114 LEU D 119 1 N PHE D 114 O LEU D 157 SHEET 11 F12 LEU D 46 ASN D 51 1 N ILE D 50 O LEU D 119 SHEET 12 F12 GLU D 84 ASN D 89 1 O LYS D 88 N ILE D 49 SHEET 1 G 3 GLY C 122 GLU C 123 0 SHEET 2 G 3 ILE C 126 GLY C 129 -1 O ILE C 126 N GLU C 123 SHEET 3 G 3 GLY C 132 ASP C 135 -1 O GLY C 132 N GLY C 129 SHEET 1 H 2 ARG C 207 ASN C 208 0 SHEET 2 H 2 GLY C 212 SER C 213 -1 O GLY C 212 N ASN C 208 SHEET 1 I 3 GLY D 122 GLU D 123 0 SHEET 2 I 3 ILE D 126 GLY D 129 -1 O ILE D 126 N GLU D 123 SHEET 3 I 3 GLY D 132 ASP D 135 -1 O GLY D 132 N GLY D 129 LINK C ALA A 162 N OCS A 163 1555 1555 1.33 LINK C OCS A 163 N ARG A 164 1555 1555 1.33 LINK C ALA B 162 N OCS B 163 1555 1555 1.33 LINK C OCS B 163 N ARG B 164 1555 1555 1.33 LINK C ALA C 162 N OCS C 163 1555 1555 1.33 LINK C OCS C 163 N ARG C 164 1555 1555 1.34 LINK C ALA D 162 N OCS D 163 1555 1555 1.33 LINK C OCS D 163 N ARG D 164 1555 1555 1.33 SITE 1 AC1 8 OCS A 163 THR A 166 LEU A 168 TYR A 204 SITE 2 AC1 8 THR C 166 LEU C 168 TYR C 204 THR C 255 CRYST1 65.521 95.984 180.528 90.00 90.00 90.00 P 21 21 21 16 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 0.015262 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010418 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005539 0.00000