HEADER HYDROLASE/HYDROLASE INHIBITOR 25-MAY-06 2H51 TITLE CRYSTAL STRUCTURE OF HUMAN CASPASE-1 (GLU390->ASP AND ARG286->LYS) IN TITLE 2 COMPLEX WITH 3-[2-(2-BENZYLOXYCARBONYLAMINO-3-METHYL-BUTYRYLAMINO)- TITLE 3 PROPIONYLAMINO]-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 MUTATION: YES; COMPND 15 MOL_ID: 3; COMPND 16 MOLECULE: N-[(BENZYLOXY)CARBONYL]-L-VALYL-N-[(2S)-1-CARBOXY-4-FLUORO- COMPND 17 3-OXOBUTAN-2-YL]-L-ALANINAMIDE; 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 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 7 30-AUG-23 2H51 1 REMARK REVDAT 6 20-OCT-21 2H51 1 SEQADV LINK REVDAT 5 30-MAY-12 2H51 1 DBREF REVDAT 4 13-JUL-11 2H51 1 VERSN REVDAT 3 24-FEB-09 2H51 1 VERSN REVDAT 2 30-SEP-08 2H51 1 JRNL REVDAT 1 11-MAR-08 2H51 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. 2.10 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) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.8 REMARK 3 NUMBER OF REFLECTIONS : 15528 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) : 0.182 REMARK 3 R VALUE (WORKING SET) : 0.180 REMARK 3 FREE R VALUE : 0.236 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 834 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) : 2.10 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.17 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1232 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.1960 REMARK 3 BIN FREE R VALUE SET COUNT : 70 REMARK 3 BIN FREE R VALUE : 0.2270 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2041 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 215 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) : 16.59 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.36000 REMARK 3 B22 (A**2) : -0.36000 REMARK 3 B33 (A**2) : 0.72000 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): 0.234 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.198 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.120 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.468 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.946 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.907 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2113 ; 0.008 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2848 ; 1.001 ; 1.960 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 251 ; 5.635 ; 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): 322 ; 0.069 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1560 ; 0.003 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1005 ; 0.183 ; 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): 194 ; 0.117 ; 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): 62 ; 0.140 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 21 ; 0.149 ; 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): 1272 ; 1.793 ; 2.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2074 ; 2.983 ; 5.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 841 ; 2.448 ; 2.500 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 773 ; 3.698 ; 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 128 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): 60.2668 48.2601 32.0748 REMARK 3 T TENSOR REMARK 3 T11: 0.0171 T22: 0.0419 REMARK 3 T33: 0.0308 T12: -0.0118 REMARK 3 T13: -0.0013 T23: -0.0131 REMARK 3 L TENSOR REMARK 3 L11: 1.0544 L22: 0.9673 REMARK 3 L33: 0.8846 L12: -0.0089 REMARK 3 L13: -0.0886 L23: -0.0965 REMARK 3 S TENSOR REMARK 3 S11: -0.0121 S12: 0.0977 S13: -0.0741 REMARK 3 S21: -0.0405 S22: 0.0119 S23: 0.0340 REMARK 3 S31: 0.0915 S32: -0.1617 S33: 0.0002 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 2H51 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_1000037937. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-MAR-05 REMARK 200 TEMPERATURE (KELVIN) : 120 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL1-5 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.16 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL, PARALLEL REMARK 200 OPTICS : RH COATED BENT CYLINDRICAL REMARK 200 MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : CRYSTALCLEAR REMARK 200 DATA SCALING SOFTWARE : D*TREK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16666 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 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 (%) : 95.6 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) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.17 REMARK 200 COMPLETENESS FOR SHELL (%) : 82.7 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 (%): 47.55 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.35 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M PIPES, 200 MM (NH4)2SO4, 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 70.77200 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 31.58200 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 31.58200 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 106.15800 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 31.58200 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 31.58200 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 35.38600 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 31.58200 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 31.58200 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 106.15800 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 31.58200 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 31.58200 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 35.38600 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 70.77200 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: 17340 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20280 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -103.0 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 126.32800 REMARK 350 BIOMT2 2 -1.000000 0.000000 0.000000 126.32800 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 70.77200 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 465 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 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 0.193 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 B 365 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 ASP B 336 -15.02 86.09 REMARK 500 PRO B 380 46.64 -79.64 REMARK 500 PHE B 401 58.80 39.76 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: 2H44 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN CASPASE-1 (ARG286->LYS) 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: 2H4W RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN CASPASE-1 (GLU390->ASP) IN COMPLEX WITH3- REMARK 900 [2-(2-BENZYLOXYCARBONYLAMINO-3-METHYL-BUTYRYLAMINO)-PROPIONYLAMINO]- REMARK 900 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 2H51 A 120 297 UNP P29466 CASP1_HUMAN 120 297 DBREF 2H51 B 317 404 UNP P29466 CASP1_HUMAN 317 404 DBREF 2H51 C 1 5 PDB 2H51 2H51 1 5 SEQADV 2H51 LYS A 286 UNP P29466 ARG 286 ENGINEERED MUTATION SEQADV 2H51 ASP B 390 UNP P29466 GLU 390 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 ASP 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 *215(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 ASN A 266 1 10 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 LYS A 203 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 PHE A 234 SHEET 5 A 6 PHE B 327 CYS B 331 1 O PHE B 330 N ILE A 280 SHEET 6 A 6 THR B 388 ASP 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 1.81 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 12 ARG A 179 SER A 236 HIS A 237 GLY A 238 SITE 2 AC1 12 GLN A 283 CYS A 285 SER B 339 TRP B 340 SITE 3 AC1 12 ARG B 341 HIS B 342 ARG B 383 HOH C 535 CRYST1 63.164 63.164 141.544 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 0.015832 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015832 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007065 0.00000