HEADER HYDROLASE/PEPTIDE 20-SEP-11 4A1X TITLE CO-COMPLEX STRUCTURE OF NS3-4A PROTEASE WITH THE INHIBITORY PEPTIDE TITLE 2 CP5-46-A (SYNCHROTRON DATA) COMPND MOL_ID: 1; COMPND 2 MOLECULE: NONSTRUCTURAL PROTEIN 4A, SERINE PROTEASE NS3; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: RESIDUES 1678-1690,1028-1206; COMPND 5 SYNONYM: NS3-4A PROTEASE, NS4A, HEPACIVIRIN, NS3P, P70; COMPND 6 EC: 3.4.21.98, 3.6.1.15, 3.6.4.13; COMPND 7 ENGINEERED: YES; COMPND 8 OTHER_DETAILS: FUSION PROTEIN OF 4A (1678-1690) WITH NS3 (1028-1206); COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: CP5-46-A PEPTIDE; COMPND 11 CHAIN: C, D; COMPND 12 ENGINEERED: YES; COMPND 13 OTHER_DETAILS: DERIVED FROM PEPTIDE LIBRARY SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HEPATITIS C VIRUS SUBTYPE 1B; SOURCE 3 ORGANISM_TAXID: 31647; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_VARIANT: ROSETTA2; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PET28C; SOURCE 10 OTHER_DETAILS: HCV REPLICON I389/NS3-3'UTR (AJ242654); SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 14 ORGANISM_TAXID: 32630; SOURCE 15 OTHER_DETAILS: DERIVED FROM PEPTIDE LIBRARY KEYWDS HYDROLASE-PEPTIDE COMPLEX, UNMODIFIED INHIBITORY PEPTIDES EXPDTA X-RAY DIFFRACTION AUTHOR S.SCHMELZ,J.KUEGLER,J.COLLINS,D.HEINZ REVDAT 4 16-OCT-24 4A1X 1 REMARK REVDAT 3 20-DEC-23 4A1X 1 REMARK SHEET LINK REVDAT 2 05-FEB-14 4A1X 1 SOURCE JRNL REMARK SITE REVDAT 2 2 1 MASTER REVDAT 1 19-SEP-12 4A1X 0 JRNL AUTH J.KUGLER,S.SCHMELZ,J.GENTZSCH,S.HAID,E.POLLMANN, JRNL AUTH 2 J.VAN DEN HEUVEL,R.FRANKE,T.PIETSCHMANN,D.W.HEINZ,J.COLLINS JRNL TITL HIGH AFFINITY PEPTIDE INHIBITORS OF THE HEPATITIS C VIRUS JRNL TITL 2 NS3-4A PROTEASE REFRACTORY TO COMMON RESISTANT MUTANTS. JRNL REF J.BIOL.CHEM. V. 287 39224 2012 JRNL REFN ISSN 0021-9258 JRNL PMID 22965230 JRNL DOI 10.1074/JBC.M112.393843 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.6.0117 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) : 80.82 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 80.8 REMARK 3 NUMBER OF REFLECTIONS : 30425 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) : 0.184 REMARK 3 R VALUE (WORKING SET) : 0.182 REMARK 3 FREE R VALUE : 0.182 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1619 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) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.95 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2178 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.70 REMARK 3 BIN R VALUE (WORKING SET) : 0.2560 REMARK 3 BIN FREE R VALUE SET COUNT : 131 REMARK 3 BIN FREE R VALUE : 0.2950 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3065 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 15 REMARK 3 SOLVENT ATOMS : 193 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 30.17 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.09 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.39000 REMARK 3 B22 (A**2) : -0.39000 REMARK 3 B33 (A**2) : 0.59000 REMARK 3 B12 (A**2) : -0.20000 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): 0.159 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.140 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.098 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.319 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.957 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.942 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3268 ; 0.008 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4478 ; 1.316 ; 1.972 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 449 ; 6.072 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 108 ;23.495 ;21.852 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 500 ;13.704 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 28 ;14.122 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 523 ; 0.089 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2486 ; 0.006 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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 : 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 : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS. REMARK 4 REMARK 4 4A1X COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 20-SEP-11. REMARK 100 THE DEPOSITION ID IS D_1290049722. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-JUN-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : BESSY REMARK 200 BEAMLINE : 14.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.91841 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 32044 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 80.800 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.700 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : 0.07000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 14.6000 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) : 1.95 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7 REMARK 200 DATA REDUNDANCY IN SHELL : 3.70 REMARK 200 R MERGE FOR SHELL (I) : 0.59000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 1DXP REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.91 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.32 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M MES PH 6.0 OR 0.1 M NA CITRATE REMARK 280 PH 5.1 AND 2.2M KCL, 5% ISOPROPANOL. REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 27.46667 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 54.93333 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 41.20000 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 68.66667 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 13.73333 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: 2690 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9160 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -105.3 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 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: 2530 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9330 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -103.2 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, 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 GLY A -2 REMARK 465 LYS A -1 REMARK 465 GLY A 0 REMARK 465 GLY A 1 REMARK 465 GLY A 181 REMARK 465 SER A 182 REMARK 465 HIS A 183 REMARK 465 HIS A 184 REMARK 465 HIS A 185 REMARK 465 HIS A 186 REMARK 465 HIS A 187 REMARK 465 HIS A 188 REMARK 465 GLY B -2 REMARK 465 LYS B -1 REMARK 465 SER B 182 REMARK 465 HIS B 183 REMARK 465 HIS B 184 REMARK 465 HIS B 185 REMARK 465 HIS B 186 REMARK 465 HIS B 187 REMARK 465 HIS B 188 REMARK 465 GLY C 1 REMARK 465 GLU C 2 REMARK 465 LEU C 3 REMARK 465 ASP C 21 REMARK 465 GLY D 1 REMARK 465 GLU D 2 REMARK 465 LEU D 3 REMARK 465 GLY D 4 REMARK 465 ARG D 5 REMARK 465 ASP D 21 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 ARG A 180 CG CD NE CZ NH1 NH2 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 OD2 ASP A 25 O HOH A 2007 2.16 REMARK 500 OG SER B 139 O HOH B 2053 2.17 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 PHE A 43 -168.35 -173.68 REMARK 500 THR B 38 -169.71 -103.44 REMARK 500 PHE B 43 -169.95 -173.86 REMARK 500 LEU C 9 50.56 -118.20 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1181 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 97 SG REMARK 620 2 CYS A 99 SG 97.1 REMARK 620 3 CYS A 145 SG 110.3 121.1 REMARK 620 4 HOH A2067 O 113.7 108.7 106.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B1182 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 97 SG REMARK 620 2 CYS B 99 SG 96.9 REMARK 620 3 CYS B 145 SG 104.4 118.7 REMARK 620 4 HOH B2068 O 115.8 111.3 109.4 REMARK 620 N 1 2 3 REMARK 700 REMARK 700 SHEET REMARK 700 DETERMINATION METHOD: DSSP REMARK 700 THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS REMARK 700 BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY REMARK 700 A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS REMARK 700 ARE IDENTICAL. REMARK 700 THE SHEETS PRESENTED AS "BB" IN EACH CHAIN ON SHEET RECORDS REMARK 700 BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY REMARK 700 A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS REMARK 700 ARE IDENTICAL. REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 1181 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 1182 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 1183 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 1184 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 1185 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 1186 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 1187 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 1188 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 1182 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL B 1183 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL B 1184 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL B 1185 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL B 1186 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL B 1187 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL B 1188 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1W3C RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE HEPATITIS C VIRUS NS3 PROTEASE IN COMPLEX REMARK 900 WITH A PEPTIDOMIMETIC INHIBITOR REMARK 900 RELATED ID: 1DXP RELATED DB: PDB REMARK 900 INHIBITION OF THE HEPATITIS C VIRUS NS3/4A PROTEASE. THE REMARK 900 CRYSTALSTRUCTURES OF TWO PROTEASE-INHIBITOR COMPLEXES REMARK 900 RELATED ID: 1DY8 RELATED DB: PDB REMARK 900 INHIBITION OF THE HEPATITIS C VIRUS NS3/4A PROTEASE. THE REMARK 900 CRYSTALSTRUCTURES OF TWO PROTEASE-INHIBITOR COMPLEXES (INHIBITOR II) REMARK 900 RELATED ID: 4A1T RELATED DB: PDB REMARK 900 CO-COMPLEX OF THE OF NS3-4A PROTEASE WITH THE INHIBITORY PEPTIDE REMARK 900 CP5-46-A (IN-HOUSE DATA) REMARK 900 RELATED ID: 1DY9 RELATED DB: PDB REMARK 900 INHIBITION OF THE HEPATITIS C VIRUS NS3/4A PROTEASE. THE REMARK 900 CRYSTALSTRUCTURES OF TWO PROTEASE-INHIBITOR COMPLEXES (INHIBITOR I) REMARK 900 RELATED ID: 4A1V RELATED DB: PDB REMARK 900 CO-COMPLEX STRUCTURE OF NS3-4A PROTEASE WITH THE OPTIMIZED REMARK 900 INHIBITORY PEPTIDE CP5-46A-4D5E REMARK 999 REMARK 999 SEQUENCE REMARK 999 SEQUENCE DISCREPANCIES HAVE BEEN INDICATED BY AUTHOR AS REMARK 999 NATURAL VARIANTS, AS THE REPLICON WAS CONSTRUCTED FROM THE REMARK 999 CONSENSUS-GENOME OF HCV GENOTYPE 1B. DBREF 4A1X A -14 -2 UNP P26662 POLG_HCVJA 1678 1690 DBREF 4A1X A 2 180 UNP P26662 POLG_HCVJA 1028 1206 DBREF 4A1X A -14 -2 UNP P26662 POLG_HCVJA 1678 1690 DBREF 4A1X B 2 180 UNP P26662 POLG_HCVJA 1028 1206 DBREF 4A1X C 1 21 PDB 4A1X 4A1X 1 21 DBREF 4A1X D 1 21 PDB 4A1X 4A1X 1 21 SEQADV 4A1X LYS A -1 UNP P26662 LINKER SEQADV 4A1X GLY A 0 UNP P26662 LINKER SEQADV 4A1X GLY A 1 UNP P26662 LINKER SEQADV 4A1X GLY A 181 UNP P26662 EXPRESSION TAG SEQADV 4A1X SER A 182 UNP P26662 EXPRESSION TAG SEQADV 4A1X HIS A 183 UNP P26662 EXPRESSION TAG SEQADV 4A1X HIS A 184 UNP P26662 EXPRESSION TAG SEQADV 4A1X HIS A 185 UNP P26662 EXPRESSION TAG SEQADV 4A1X HIS A 186 UNP P26662 EXPRESSION TAG SEQADV 4A1X HIS A 187 UNP P26662 EXPRESSION TAG SEQADV 4A1X HIS A 188 UNP P26662 EXPRESSION TAG SEQADV 4A1X ARG A 26 UNP P26662 LYS 1052 SEE REMARK 999 SEQADV 4A1X GLU A 30 UNP P26662 ASP 1056 SEE REMARK 999 SEQADV 4A1X VAL A 36 UNP P26662 LEU 1062 SEE REMARK 999 SEQADV 4A1X GLN A 86 UNP P26662 PRO 1112 SEE REMARK 999 SEQADV 4A1X LEU A 94 UNP P26662 MET 1120 SEE REMARK 999 SEQADV 4A1X ILE A 114 UNP P26662 VAL 1140 VARIANT SEQADV 4A1X VAL A 132 UNP P26662 ILE 1158 VARIANT SEQADV 4A1X ALA A 150 UNP P26662 VAL 1176 SEE REMARK 999 SEQADV 4A1X VAL A 170 UNP P26662 ILE 1196 SEE REMARK 999 SEQADV 4A1X LYS B -1 UNP P26662 LINKER SEQADV 4A1X GLY B 0 UNP P26662 LINKER SEQADV 4A1X GLY B 1 UNP P26662 LINKER SEQADV 4A1X GLY B 181 UNP P26662 EXPRESSION TAG SEQADV 4A1X SER B 182 UNP P26662 EXPRESSION TAG SEQADV 4A1X HIS B 183 UNP P26662 EXPRESSION TAG SEQADV 4A1X HIS B 184 UNP P26662 EXPRESSION TAG SEQADV 4A1X HIS B 185 UNP P26662 EXPRESSION TAG SEQADV 4A1X HIS B 186 UNP P26662 EXPRESSION TAG SEQADV 4A1X HIS B 187 UNP P26662 EXPRESSION TAG SEQADV 4A1X HIS B 188 UNP P26662 EXPRESSION TAG SEQADV 4A1X ARG B 26 UNP P26662 LYS 1052 SEE REMARK 999 SEQADV 4A1X GLU B 30 UNP P26662 ASP 1056 SEE REMARK 999 SEQADV 4A1X VAL B 36 UNP P26662 LEU 1062 SEE REMARK 999 SEQADV 4A1X GLN B 86 UNP P26662 PRO 1112 SEE REMARK 999 SEQADV 4A1X LEU B 94 UNP P26662 MET 1120 SEE REMARK 999 SEQADV 4A1X ILE B 114 UNP P26662 VAL 1140 SEE REMARK 999 SEQADV 4A1X VAL B 132 UNP P26662 ILE 1158 VARIANT SEQADV 4A1X ALA B 150 UNP P26662 VAL 1176 SEE REMARK 999 SEQADV 4A1X VAL B 170 UNP P26662 ILE 1196 SEE REMARK 999 SEQRES 1 A 203 GLY SER VAL VAL ILE VAL GLY ARG ILE ILE LEU SER GLY SEQRES 2 A 203 LYS GLY GLY PRO ILE THR ALA TYR SER GLN GLN THR ARG SEQRES 3 A 203 GLY LEU LEU GLY CYS ILE ILE THR SER LEU THR GLY ARG SEQRES 4 A 203 ASP ARG ASN GLN VAL GLU GLY GLU VAL GLN VAL VAL SER SEQRES 5 A 203 THR ALA THR GLN SER PHE LEU ALA THR CYS VAL ASN GLY SEQRES 6 A 203 VAL CYS TRP THR VAL TYR HIS GLY ALA GLY SER LYS THR SEQRES 7 A 203 LEU ALA GLY PRO LYS GLY PRO ILE THR GLN MET TYR THR SEQRES 8 A 203 ASN VAL ASP GLN ASP LEU VAL GLY TRP GLN ALA PRO PRO SEQRES 9 A 203 GLY ALA ARG SER LEU THR PRO CYS THR CYS GLY SER SER SEQRES 10 A 203 ASP LEU TYR LEU VAL THR ARG HIS ALA ASP VAL ILE PRO SEQRES 11 A 203 VAL ARG ARG ARG GLY ASP SER ARG GLY SER LEU LEU SER SEQRES 12 A 203 PRO ARG PRO VAL SER TYR LEU LYS GLY SER SER GLY GLY SEQRES 13 A 203 PRO LEU LEU CYS PRO SER GLY HIS ALA VAL GLY ILE PHE SEQRES 14 A 203 ARG ALA ALA VAL CYS THR ARG GLY VAL ALA LYS ALA VAL SEQRES 15 A 203 ASP PHE VAL PRO VAL GLU SER MET GLU THR THR MET ARG SEQRES 16 A 203 GLY SER HIS HIS HIS HIS HIS HIS SEQRES 1 B 203 GLY SER VAL VAL ILE VAL GLY ARG ILE ILE LEU SER GLY SEQRES 2 B 203 LYS GLY GLY PRO ILE THR ALA TYR SER GLN GLN THR ARG SEQRES 3 B 203 GLY LEU LEU GLY CYS ILE ILE THR SER LEU THR GLY ARG SEQRES 4 B 203 ASP ARG ASN GLN VAL GLU GLY GLU VAL GLN VAL VAL SER SEQRES 5 B 203 THR ALA THR GLN SER PHE LEU ALA THR CYS VAL ASN GLY SEQRES 6 B 203 VAL CYS TRP THR VAL TYR HIS GLY ALA GLY SER LYS THR SEQRES 7 B 203 LEU ALA GLY PRO LYS GLY PRO ILE THR GLN MET TYR THR SEQRES 8 B 203 ASN VAL ASP GLN ASP LEU VAL GLY TRP GLN ALA PRO PRO SEQRES 9 B 203 GLY ALA ARG SER LEU THR PRO CYS THR CYS GLY SER SER SEQRES 10 B 203 ASP LEU TYR LEU VAL THR ARG HIS ALA ASP VAL ILE PRO SEQRES 11 B 203 VAL ARG ARG ARG GLY ASP SER ARG GLY SER LEU LEU SER SEQRES 12 B 203 PRO ARG PRO VAL SER TYR LEU LYS GLY SER SER GLY GLY SEQRES 13 B 203 PRO LEU LEU CYS PRO SER GLY HIS ALA VAL GLY ILE PHE SEQRES 14 B 203 ARG ALA ALA VAL CYS THR ARG GLY VAL ALA LYS ALA VAL SEQRES 15 B 203 ASP PHE VAL PRO VAL GLU SER MET GLU THR THR MET ARG SEQRES 16 B 203 GLY SER HIS HIS HIS HIS HIS HIS SEQRES 1 C 21 GLY GLU LEU GLY ARG LEU VAL TYR LEU LEU ASP GLY PRO SEQRES 2 C 21 GLY TYR ASP PRO ILE HIS CYS ASP SEQRES 1 D 21 GLY GLU LEU GLY ARG LEU VAL TYR LEU LEU ASP GLY PRO SEQRES 2 D 21 GLY TYR ASP PRO ILE HIS CYS ASP HET ZN A1181 1 HET CL A1182 1 HET CL A1183 1 HET CL A1184 1 HET CL A1185 1 HET CL A1186 1 HET CL A1187 1 HET CL A1188 1 HET ZN B1182 1 HET CL B1183 1 HET CL B1184 1 HET CL B1185 1 HET CL B1186 1 HET CL B1187 1 HET CL B1188 1 HETNAM ZN ZINC ION HETNAM CL CHLORIDE ION FORMUL 5 ZN 2(ZN 2+) FORMUL 6 CL 13(CL 1-) FORMUL 20 HOH *193(H2 O) HELIX 1 1 GLY A 12 GLY A 23 1 12 HELIX 2 2 TYR A 56 GLY A 60 1 5 HELIX 3 3 SER A 133 LYS A 136 5 4 HELIX 4 4 VAL A 172 ARG A 180 1 9 HELIX 5 5 GLY B 12 GLY B 23 1 12 HELIX 6 6 TYR B 56 GLY B 60 1 5 HELIX 7 7 SER B 133 LYS B 136 5 4 HELIX 8 8 VAL B 172 GLY B 181 1 10 SHEET 1 AA 7 ALA A 5 GLN A 9 0 SHEET 2 AA 7 VAL A -11 LEU A -4 -1 O ARG A -7 N GLN A 8 SHEET 3 AA 7 VAL A 33 SER A 37 -1 O VAL A 33 N ILE A -6 SHEET 4 AA 7 SER A 42 VAL A 48 -1 O PHE A 43 N VAL A 36 SHEET 5 AA 7 VAL A 51 VAL A 55 -1 O VAL A 51 N VAL A 48 SHEET 6 AA 7 LEU A 82 GLN A 86 -1 O VAL A 83 N THR A 54 SHEET 7 AA 7 TYR A 75 ASN A 77 -1 O TYR A 75 N GLY A 84 SHEET 1 AB 7 ASP A 103 VAL A 107 0 SHEET 2 AB 7 VAL A 113 GLY A 120 -1 O ILE A 114 N LEU A 106 SHEET 3 AB 7 ARG A 123 PRO A 131 -1 O ARG A 123 N ARG A 119 SHEET 4 AB 7 VAL A 163 PRO A 171 -1 O ALA A 164 N ARG A 130 SHEET 5 AB 7 ALA A 150 THR A 160 1 O ILE A 153 N VAL A 170 SHEET 6 AB 7 PRO A 142 LEU A 144 -1 O LEU A 143 N VAL A 151 SHEET 7 AB 7 ASP A 103 VAL A 107 0 SHEET 1 BA 7 THR B 4 GLN B 9 0 SHEET 2 BA 7 VAL B -11 SER B -3 -1 O ARG B -7 N GLN B 8 SHEET 3 BA 7 VAL B 33 SER B 37 -1 O VAL B 33 N ILE B -6 SHEET 4 BA 7 SER B 42 VAL B 48 -1 O PHE B 43 N VAL B 36 SHEET 5 BA 7 VAL B 51 VAL B 55 -1 O VAL B 51 N VAL B 48 SHEET 6 BA 7 LEU B 82 GLN B 86 -1 O VAL B 83 N THR B 54 SHEET 7 BA 7 TYR B 75 ASN B 77 -1 O TYR B 75 N GLY B 84 SHEET 1 BB 7 ASP B 103 VAL B 107 0 SHEET 2 BB 7 VAL B 113 ARG B 118 -1 O ILE B 114 N LEU B 106 SHEET 3 BB 7 ARG B 123 PRO B 131 -1 O SER B 125 N ARG B 117 SHEET 4 BB 7 VAL B 163 PRO B 171 -1 O ALA B 164 N ARG B 130 SHEET 5 BB 7 ALA B 150 THR B 160 -1 O ILE B 153 N VAL B 170 SHEET 6 BB 7 PRO B 142 LEU B 144 -1 O LEU B 143 N VAL B 151 SHEET 7 BB 7 ASP B 103 VAL B 107 -1 O TYR B 105 N LEU B 144 SSBOND 1 CYS A 47 CYS A 52 1555 1555 2.06 LINK SG CYS A 97 ZN ZN A1181 1555 1555 2.31 LINK SG CYS A 99 ZN ZN A1181 1555 1555 2.39 LINK SG CYS A 145 ZN ZN A1181 1555 1555 2.37 LINK ZN ZN A1181 O HOH A2067 1555 1555 2.32 LINK SG CYS B 97 ZN ZN B1182 1555 1555 2.42 LINK SG CYS B 99 ZN ZN B1182 1555 1555 2.57 LINK SG CYS B 145 ZN ZN B1182 1555 1555 2.62 LINK ZN ZN B1182 O HOH B2068 1555 1555 2.34 CISPEP 1 ARG B 180 GLY B 181 0 -0.25 SITE 1 AC1 4 CYS A 97 CYS A 99 CYS A 145 HOH A2067 SITE 1 AC2 3 THR A 38 THR A 40 GLN A 41 SITE 1 AC3 4 ARG A 11 GLY A 12 GLY A 15 PRO A 70 SITE 1 AC4 5 GLY A -14 GLN A 9 GLY A 12 LEU A 13 SITE 2 AC4 5 HOH C2006 SITE 1 AC5 2 ARG A 26 ARG B 26 SITE 1 AC6 3 GLY A 60 SER A 61 LYS A 62 SITE 1 AC7 3 ARG A 11 ARG A 26 HOH A2022 SITE 1 AC8 3 VAL A 132 SER A 133 GLY A 162 SITE 1 AC9 4 CYS B 97 CYS B 99 CYS B 145 HOH B2068 SITE 1 BC1 3 SER B 61 LYS B 62 HOH D2003 SITE 1 BC2 4 PRO B 131 VAL B 132 SER B 133 GLY B 162 SITE 1 BC3 5 GLY B -14 THR B 38 ALA B 39 LYS B 62 SITE 2 BC3 5 HOH B2043 SITE 1 BC4 4 GLY B -14 GLN B 9 GLY B 12 LEU B 13 SITE 1 BC5 3 LYS A 68 ASN B 27 GLN B 28 SITE 1 BC6 4 ARG B 11 GLY B 12 GLY B 15 PRO B 70 CRYST1 93.320 93.320 82.400 90.00 90.00 120.00 P 61 12 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 0.010716 0.006187 0.000000 0.00000 SCALE2 0.000000 0.012374 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012136 0.00000