HEADER HYDROLASE/HYDROLASE INHIBITOR 25-MAY-06 2H4Y TITLE CRYSTAL STRUCTURE OF HUMAN CASPASE-1 (ARG286->LYS) IN COMPLEX WITH 3- TITLE 2 [2-(2-BENZYLOXYCARBONYLAMINO-3-METHYL-BUTYRYLAMINO)-PROPIONYLAMINO]- TITLE 3 4-OXO-PENTANOIC ACID (Z-VAD-FMK) COMPND MOL_ID: 1; COMPND 2 MOLECULE: CASPASE-1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: P20 SUBUNIT, RESIDUES 120-297; COMPND 5 EC: 3.4.22.36; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: CASPASE-1; COMPND 10 CHAIN: B; COMPND 11 FRAGMENT: P10 SUBUNIT, RESIDUES 317-404; COMPND 12 EC: 3.4.22.36; COMPND 13 ENGINEERED: YES; COMPND 14 MOL_ID: 3; COMPND 15 MOLECULE: N-[(BENZYLOXY)CARBONYL]-L-VALYL-N-[(2S)-1-CARBOXY-4-FLUORO- COMPND 16 3-OXOBUTAN-2-YL]-L-ALANINAMIDE; COMPND 17 CHAIN: C; COMPND 18 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: CASP1, IL1BC, IL1BCE; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) CODON+; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PRSET; SOURCE 11 MOL_ID: 2; SOURCE 12 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 13 ORGANISM_COMMON: HUMAN; SOURCE 14 ORGANISM_TAXID: 9606; SOURCE 15 GENE: CASP1, IL1BC, IL1BCE; SOURCE 16 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 17 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 18 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) CODON+; SOURCE 19 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 20 EXPRESSION_SYSTEM_PLASMID: PRSET; SOURCE 21 MOL_ID: 3; SOURCE 22 SYNTHETIC: YES KEYWDS ALLOSTERIC SITE, DIMER INTERFACE, HYDROLASE, HYDROLASE-HYDROLASE KEYWDS 2 INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR J.M.SCHEER,J.A.WELLS,M.J.ROMANOWSKI REVDAT 6 20-OCT-21 2H4Y 1 SEQADV LINK REVDAT 5 30-MAY-12 2H4Y 1 DBREF REVDAT 4 13-JUL-11 2H4Y 1 VERSN REVDAT 3 24-FEB-09 2H4Y 1 VERSN REVDAT 2 30-SEP-08 2H4Y 1 JRNL REVDAT 1 11-MAR-08 2H4Y 0 JRNL AUTH D.DATTA,J.M.SCHEER,M.J.ROMANOWSKI,J.A.WELLS JRNL TITL AN ALLOSTERIC CIRCUIT IN CASPASE-1. JRNL REF J.MOL.BIOL. V. 381 1157 2008 JRNL REFN ISSN 0022-2836 JRNL PMID 18590738 JRNL DOI 10.1016/J.JMB.2008.06.040 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.1.19 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) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 88.5 REMARK 3 NUMBER OF REFLECTIONS : 19735 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) : 0.205 REMARK 3 R VALUE (WORKING SET) : 0.203 REMARK 3 FREE R VALUE : 0.235 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1070 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 15 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.97 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1587 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.3010 REMARK 3 BIN FREE R VALUE SET COUNT : 95 REMARK 3 BIN FREE R VALUE : 0.3380 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2019 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 189 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.98 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.67000 REMARK 3 B22 (A**2) : -0.67000 REMARK 3 B33 (A**2) : 1.33000 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): 0.186 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.159 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.117 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.111 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.945 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.924 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2084 ; 0.006 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2808 ; 0.879 ; 1.959 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 247 ; 5.227 ; 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): 317 ; 0.059 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1536 ; 0.002 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 984 ; 0.161 ; 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): 172 ; 0.079 ; 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): 63 ; 0.140 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 28 ; 0.071 ; 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): 1251 ; 1.321 ; 2.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2043 ; 2.305 ; 5.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 833 ; 1.537 ; 2.500 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 765 ; 2.457 ; 5.000 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): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL 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 : 1 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 4 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 132 A 145 REMARK 3 RESIDUE RANGE : A 149 A 297 REMARK 3 RESIDUE RANGE : B 318 B 404 REMARK 3 RESIDUE RANGE : A 501 A 501 REMARK 3 ORIGIN FOR THE GROUP (A): 60.5700 48.4960 32.0397 REMARK 3 T TENSOR REMARK 3 T11: 0.0398 T22: 0.0418 REMARK 3 T33: 0.0309 T12: -0.0067 REMARK 3 T13: -0.0107 T23: -0.0165 REMARK 3 L TENSOR REMARK 3 L11: 0.7974 L22: 0.7509 REMARK 3 L33: 0.6765 L12: 0.1887 REMARK 3 L13: 0.0466 L23: -0.0831 REMARK 3 S TENSOR REMARK 3 S11: -0.0139 S12: 0.0489 S13: -0.0693 REMARK 3 S21: -0.0273 S22: 0.0248 S23: -0.0015 REMARK 3 S31: 0.0633 S32: -0.1155 S33: -0.0109 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : 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 2H4Y COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-JUN-06. REMARK 100 THE DEPOSITION ID IS D_1000037934. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-MAR-05 REMARK 200 TEMPERATURE (KELVIN) : 110 REMARK 200 PH : 6.0 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 : RIGAKU RU300 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : NI FILTER REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : CRYSTALCLEAR REMARK 200 DATA SCALING SOFTWARE : D*TREK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 22772 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 5.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.8 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.97 REMARK 200 COMPLETENESS FOR SHELL (%) : 90.6 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 1SC3 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.85 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.36 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M PIPES, 200 MM LI2SO4, 25% PEG REMARK 280 2000 MME, 10 MM DTT, 3 MM NAN3, 2 MM MGCL2, PH 6.0, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-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 70.80350 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 31.67150 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 31.67150 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 106.20525 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 31.67150 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 31.67150 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 35.40175 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 31.67150 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 31.67150 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 106.20525 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 31.67150 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 31.67150 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 35.40175 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 70.80350 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 300 REMARK: HETEROTETRAMER (DIMER OF TWO HETERODIMERS). EACH REMARK 300 HETERODIMER IS REPRESENTED BY CHAINS A (THE P20 SUBUNIT) AND B (THE REMARK 300 P10 SUBUNIT) OF HUMAN CASPASE-1. 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: PISA,PQS REMARK 350 TOTAL BURIED SURFACE AREA: 17290 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20140 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -96.0 KCAL/MOL 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 0.000000 -1.000000 0.000000 126.68600 REMARK 350 BIOMT2 2 -1.000000 0.000000 0.000000 126.68600 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 70.80350 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 B 430 LIES ON A SPECIAL POSITION. REMARK 400 REMARK 400 COMPOUND REMARK 400 REMARK 400 THE N-[(BENZYLOXY)CARBONYL]-L-VALYL-N-[(1S)-1-(CARBOXYMETHYL)-3- REMARK 400 FLUORO-2-OXOPROPYL]-L-ALANINAMIDE IS PEPTIDE-LIKE, A MEMBER OF REMARK 400 INHIBITOR CLASS. REMARK 400 REMARK 400 GROUP: 1 REMARK 400 NAME: N-[(BENZYLOXY)CARBONYL]-L-VALYL-N-[(1S)-1-(CARBOXYMETHYL)-3- REMARK 400 FLUORO-2-OXOPROPYL]-L-ALANINAMIDE REMARK 400 CHAIN: C 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 ASN A 120 REMARK 465 PRO A 121 REMARK 465 ALA A 122 REMARK 465 MET A 123 REMARK 465 PRO A 124 REMARK 465 THR A 125 REMARK 465 SER A 126 REMARK 465 SER A 127 REMARK 465 GLY A 128 REMARK 465 SER A 129 REMARK 465 GLU A 130 REMARK 465 GLY A 131 REMARK 465 LYS A 146 REMARK 465 GLN A 147 REMARK 465 LYS A 148 REMARK 465 ALA B 317 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 GLN A 251 CG CD OE1 NE2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 ASP C 4 C ASP C 4 O 0.192 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 ASP A 228 CB - CG - OD2 ANGL. DEV. = 5.6 DEGREES REMARK 500 ASP A 254 CB - CG - OD2 ANGL. DEV. = 5.5 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 ASP B 336 -15.44 86.05 REMARK 500 PRO B 380 45.08 -78.73 REMARK 500 PHE B 401 59.92 39.03 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 N REMARK 800 -[(BENZYLOXY)CARBONYL]-L-VALYL-N-[(2S)-1-CARBOXY-4-FLUORO- 3- REMARK 800 OXOBUTAN-2-YL]-L-ALANINAMIDE REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2FQV RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN CASPASE-1 (ARG286->ALA, GLU390->ALA) IN REMARK 900 COMPLEX WITH 3-[2-(2-BENZYLOXYCARBONYLAMINO-3-METHYL-BUTYRYLAMINO)- REMARK 900 PROPIONYLAMINO]-4-OXO-PENTANOIC ACID (Z-VAD-FMK) REMARK 900 RELATED ID: 1SC3 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE HUMAN CASPASE-1 C285A MUTANT IN COMPLEX REMARK 900 WITH MALONATE REMARK 900 RELATED ID: 2FQQ RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN CASPASE-1 (CYS285->ALA, CYS362->ALA, REMARK 900 CYS364->ALA, CYS397->ALA) IN COMPLEX WITH 1-METHYL-3- REMARK 900 TRIFLUOROMETHYL-1H-THIENO[2,3-C]PYRAZOLE-5-CARBOXYLIC ACID (2- REMARK 900 MERCAPTO-ETHYL)-AMIDE REMARK 900 RELATED ID: 2FQR RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF WILDTYPE HUMAN CASPASE-1 IN COMPLEX WITH 3-[2- REMARK 900 (2-BENZYLOXYCARBONYLAMINO-3-METHYL-BUTYRYLAMINO)-PROPIONYLAMINO]-4- REMARK 900 OXO-PENTANOIC ACID (Z-VAD-FMK) REMARK 900 RELATED ID: 2FQS RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN CASPASE-1 (ARG286->ALA) IN COMPLEX WITH REMARK 900 3-[2-(2-BENZYLOXYCARBONYLAMINO-3-METHYL-BUTYRYLAMINO)- REMARK 900 PROPIONYLAMINO]-4-OXO-PENTANOIC ACID (Z-VAD-FMK) REMARK 900 RELATED ID: 2FQU RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN CASPASE-1 (GLU390->ALA) IN COMPLEX WITH REMARK 900 3-[2-(2-BENZYLOXYCARBONYLAMINO-3-METHYL-BUTYRYLAMINO)- REMARK 900 PROPIONYLAMINO]-4-OXO-PENTANOIC ACID (Z-VAD-FMK) REMARK 900 RELATED ID: 2H48 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN CASPASE-1 (CYS362->ALA, CYS364->ALA, REMARK 900 CYS397->ALA) IN COMPLEX WITH 3-[2-(2-BENZYLOXYCARBONYLAMINO-3- REMARK 900 METHYL-BUTYRYLAMINO)-PROPIONYLAMINO]-4-OXO-PENTANOIC ACID (Z-VAD- REMARK 900 FMK) REMARK 900 RELATED ID: 2H4Y RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN CASPASE-1 (GLU390->ASP) IN COMPLEX WITH REMARK 900 3-[2-(2-BENZYLOXYCARBONYLAMINO-3-METHYL-BUTYRYLAMINO)- REMARK 900 PROPIONYLAMINO]-4-OXO-PENTANOIC ACID (Z-VAD-FMK) REMARK 900 RELATED ID: 2H51 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN CASPASE-1 (GLU390->ASP AND ARG286->LYS) REMARK 900 IN COMPLEX WITH 3-[2-(2-BENZYLOXYCARBONYLAMINO-3-METHYL- REMARK 900 BUTYRYLAMINO)-PROPIONYLAMINO]-4-OXO-PENTANOIC ACID (Z-VAD-FMK) REMARK 900 RELATED ID: 2H54 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN CASPASE-1 (THR388->ALA) IN COMPLEX WITH REMARK 900 3-[2-(2-BENZYLOXYCARBONYLAMINO-3-METHYL-BUTYRYLAMINO)- REMARK 900 PROPIONYLAMINO]-4-OXO-PENTANOIC ACID (Z-VAD-FMK) DBREF 2H4Y A 120 297 UNP P29466 CASP1_HUMAN 120 297 DBREF 2H4Y B 317 404 UNP P29466 CASP1_HUMAN 317 404 DBREF 2H4Y C 1 5 PDB 2H4Y 2H4Y 1 5 SEQADV 2H4Y LYS A 286 UNP P29466 ARG 286 ENGINEERED MUTATION SEQRES 1 A 178 ASN PRO ALA MET PRO THR SER SER GLY SER GLU GLY ASN SEQRES 2 A 178 VAL LYS LEU CYS SER LEU GLU GLU ALA GLN ARG ILE TRP SEQRES 3 A 178 LYS GLN LYS SER ALA GLU ILE TYR PRO ILE MET ASP LYS SEQRES 4 A 178 SER SER ARG THR ARG LEU ALA LEU ILE ILE CYS ASN GLU SEQRES 5 A 178 GLU PHE ASP SER ILE PRO ARG ARG THR GLY ALA GLU VAL SEQRES 6 A 178 ASP ILE THR GLY MET THR MET LEU LEU GLN ASN LEU GLY SEQRES 7 A 178 TYR SER VAL ASP VAL LYS LYS ASN LEU THR ALA SER ASP SEQRES 8 A 178 MET THR THR GLU LEU GLU ALA PHE ALA HIS ARG PRO GLU SEQRES 9 A 178 HIS LYS THR SER ASP SER THR PHE LEU VAL PHE MET SER SEQRES 10 A 178 HIS GLY ILE ARG GLU GLY ILE CYS GLY LYS LYS HIS SER SEQRES 11 A 178 GLU GLN VAL PRO ASP ILE LEU GLN LEU ASN ALA ILE PHE SEQRES 12 A 178 ASN MET LEU ASN THR LYS ASN CYS PRO SER LEU LYS ASP SEQRES 13 A 178 LYS PRO LYS VAL ILE ILE ILE GLN ALA CYS LYS GLY ASP SEQRES 14 A 178 SER PRO GLY VAL VAL TRP PHE LYS ASP SEQRES 1 B 88 ALA ILE LYS LYS ALA HIS ILE GLU LYS ASP PHE ILE ALA SEQRES 2 B 88 PHE CYS SER SER THR PRO ASP ASN VAL SER TRP ARG HIS SEQRES 3 B 88 PRO THR MET GLY SER VAL PHE ILE GLY ARG LEU ILE GLU SEQRES 4 B 88 HIS MET GLN GLU TYR ALA CYS SER CYS ASP VAL GLU GLU SEQRES 5 B 88 ILE PHE ARG LYS VAL ARG PHE SER PHE GLU GLN PRO ASP SEQRES 6 B 88 GLY ARG ALA GLN MET PRO THR THR GLU ARG VAL THR LEU SEQRES 7 B 88 THR ARG CYS PHE TYR LEU PHE PRO GLY HIS SEQRES 1 C 5 PHQ VAL ALA ASP CF0 HET PHQ C 1 10 HET CF0 C 5 1 HETNAM PHQ BENZYL CHLOROCARBONATE HETNAM CF0 FLUOROMETHANE HETSYN CF0 FLUORO METHYL GROUP FORMUL 3 PHQ C8 H7 CL O2 FORMUL 3 CF0 C H3 F FORMUL 4 HOH *189(H2 O) HELIX 1 1 SER A 137 TRP A 145 1 9 HELIX 2 2 GLY A 181 LEU A 196 1 16 HELIX 3 3 THR A 207 HIS A 220 1 14 HELIX 4 4 ARG A 221 SER A 227 5 7 HELIX 5 5 GLN A 257 LEU A 265 1 9 HELIX 6 6 CYS A 270 LYS A 274 5 5 HELIX 7 7 VAL B 348 ALA B 361 1 14 HELIX 8 8 ASP B 365 PHE B 377 1 13 SHEET 1 A 6 SER A 199 LYS A 204 0 SHEET 2 A 6 LEU A 164 CYS A 169 1 N ILE A 167 O ASP A 201 SHEET 3 A 6 THR A 230 MET A 235 1 O VAL A 233 N ILE A 168 SHEET 4 A 6 LYS A 278 GLN A 283 1 O ILE A 281 N LEU A 232 SHEET 5 A 6 PHE B 327 CYS B 331 1 O ILE B 328 N ILE A 280 SHEET 6 A 6 THR B 388 GLU B 390 -1 O THR B 388 N CYS B 331 SHEET 1 B 3 GLY A 238 ILE A 239 0 SHEET 2 B 3 GLY A 242 CYS A 244 -1 O GLY A 242 N ILE A 239 SHEET 3 B 3 ILE A 255 LEU A 256 -1 O LEU A 256 N ILE A 243 SHEET 1 C 2 ARG B 341 HIS B 342 0 SHEET 2 C 2 GLY B 346 SER B 347 -1 O GLY B 346 N HIS B 342 LINK SG CYS A 285 C1 CF0 C 5 1555 1555 1.82 LINK C1 PHQ C 1 N VAL C 2 1555 1555 1.33 LINK C ASP C 4 C1 CF0 C 5 1555 1555 1.53 SITE 1 AC1 14 ARG A 179 SER A 236 HIS A 237 GLY A 238 SITE 2 AC1 14 GLN A 283 CYS A 285 SER B 339 TRP B 340 SITE 3 AC1 14 ARG B 341 HIS B 342 PRO B 343 ARG B 383 SITE 4 AC1 14 HOH C 528 HOH C 579 CRYST1 63.343 63.343 141.607 90.00 90.00 90.00 P 43 21 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 0.015787 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015787 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007062 0.00000 MASTER 443 0 2 8 11 0 4 6 0 0 0 22 END