HEADER HYDROLASE/HYDROLASE INHIBITOR 31-JAN-00 1DY9 TITLE INHIBITION OF THE HEPATITIS C VIRUS NS3/4A PROTEASE. THE CRYSTAL TITLE 2 STRUCTURES OF TWO PROTEASE-INHIBITOR COMPLEXES (INHIBITOR I) COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEASE/HELICASE NS3 (P70); COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: PROTEASE; COMPND 5 EC: 3.4.22.-; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: NONSTRUCTURAL PROTEIN NS4A (P4); COMPND 9 CHAIN: C, D; COMPND 10 FRAGMENT: RESIDUES 956-967; COMPND 11 ENGINEERED: YES; COMPND 12 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HEPATITIS C VIRUS (ISOLATE TAIWAN); SOURCE 3 ORGANISM_TAXID: 31645; SOURCE 4 STRAIN: ISOLATE TAIWAN; SOURCE 5 GENE: HCV; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PT7-7; SOURCE 10 OTHER_DETAILS: CDNA OF HEPATITIS C VIRUS; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 ORGANISM_SCIENTIFIC: HEPATITIS C VIRUS; SOURCE 14 ORGANISM_TAXID: 31645 KEYWDS SERINE PROTEASE, NS3, NS4A, HEPATITIS C VIRUS, PROTEASE INHIBITION, KEYWDS 2 HYDROLASE-HYDROLASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR S.DI MARCO,M.RIZZI,C.VOLPARI,M.WALSH,F.NARJES,S.COLARUSSO,R.DE AUTHOR 2 FRANCESCO,V.G.MATASSA,M.SOLLAZZO REVDAT 8 06-DEC-23 1DY9 1 REMARK LINK REVDAT 7 09-OCT-19 1DY9 1 REMARK REVDAT 6 08-MAY-19 1DY9 1 REMARK LINK REVDAT 5 13-JUL-11 1DY9 1 VERSN REVDAT 4 24-FEB-09 1DY9 1 VERSN REVDAT 3 25-MAR-04 1DY9 1 JRNL REVDAT 2 28-MAR-02 1DY9 1 JRNL REVDAT 1 28-JAN-01 1DY9 0 JRNL AUTH S.DI MARCO,M.RIZZI,C.VOLPARI,M.WALSH,F.NARJES,S.COLARUSSO, JRNL AUTH 2 R.DE FRANCESCO,V.G.MATASSA,M.SOLLAZZO JRNL TITL INHIBITION OF THE HEPATITIS C VIRUS NS3/4A PROTEASE THE JRNL TITL 2 CRYSTAL STRUCTURES OF TWO PROTEASE-INHIBITOR COMPLEXES JRNL REF J.BIOL.CHEM. V. 275 7152 2000 JRNL REFN ISSN 0021-9258 JRNL PMID 10702283 JRNL DOI 10.1074/JBC.275.10.7152 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN 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 (%) : 98.2 REMARK 3 NUMBER OF REFLECTIONS : 23960 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) : 0.207 REMARK 3 R VALUE (WORKING SET) : 0.213 REMARK 3 FREE R VALUE : 0.275 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1224 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2734 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 71 REMARK 3 SOLVENT ATOMS : 213 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 37.40 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 43.50 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.220 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.210 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.097 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.620 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : 0.010 ; 0.020 REMARK 3 ANGLE DISTANCE (A) : 0.030 ; 0.040 REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : 0.030 ; 0.050 REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : 0.012 ; 0.020 REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : 0.125 ; 0.150 REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : 0.193 ; 0.300 REMARK 3 MULTIPLE TORSION (A) : 0.278 ; 0.300 REMARK 3 H-BOND (X...Y) (A) : 0.201 ; 0.300 REMARK 3 H-BOND (X-H...Y) (A) : NULL ; NULL REMARK 3 REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. REMARK 3 SPECIFIED (DEGREES) : NULL ; NULL REMARK 3 PLANAR (DEGREES) : 6.700 ; 7.000 REMARK 3 STAGGERED (DEGREES) : 20.500; 15.000 REMARK 3 TRANSVERSE (DEGREES) : 26.400; 20.000 REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 2.900 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 4.180 ; 3.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 3.770 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 5.490 ; 3.000 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1DY9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 31-JAN-00. REMARK 100 THE DEPOSITION ID IS D_1290004549. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-FEB-99 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 5.10 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-3 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.936 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : TOROIDAL MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23960 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.2 REMARK 200 DATA REDUNDANCY : 2.800 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.03500 REMARK 200 FOR THE DATA SET : 32.0000 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) : 2.14 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.4 REMARK 200 DATA REDUNDANCY IN SHELL : 2.10 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.15000 REMARK 200 FOR SHELL : 3.200 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 1DY7 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.68 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.37 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: THE NS3 PROTEIN (1MG/ML) WAS INCUBATE REMARK 280 AT 4C WITH THE NS4A COFACTOR PEPTIDE, CONTAINING A SOLUBIZING REMARK 280 LYSINE TAG AT ITS N- AND C-TERMINI(KGSVVIVGRIILSGRK), AT A MOLAR REMARK 280 RATIO OF 1:2 AND CONCENTRATED TO 290 MICROMOLAR. NS3J/4A REMARK 280 CRYSTALS, WITH A MAXIMUM SIZE OF 0.6 X 0.3 X 0.2 MM**3, WERE REMARK 280 OBTAINED BY BOTH HANGING- AND SITTING-DROP VAPOUR DIFFUSION REMARK 280 METHODS AFTER TWO WEEKS AT ROOM TEMPERATURE, WITH 3.4 M NACL, REMARK 280 10MM DTT, 0.1 M CITRATE BUFFER PH 5.1. THE TERNARY COMPLEX WITH REMARK 280 INHIBITOR WAS PREPARED BY ADDING 5.0 MM OF INIBITOR TO CRYSTALS REMARK 280 THAT WERE STABILISED IN 4.5 M NACL, 10 MM DTT, 0.1 M CITRATE REMARK 280 BUFFER, PH 5.1., PH 5.10, VAPOR DIFFUSION 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 27.45667 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 54.91333 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 41.18500 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 68.64167 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 13.72833 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PQS REMARK 350 TOTAL BURIED SURFACE AREA: 4770 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10070 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -19.4 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PQS REMARK 350 TOTAL BURIED SURFACE AREA: 4820 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10050 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -22.4 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 GLU A 176 REMARK 465 THR A 177 REMARK 465 THR A 178 REMARK 465 MET A 179 REMARK 465 ARG A 180 REMARK 465 SER A 181 REMARK 465 PRO A 182 REMARK 465 VAL A 183 REMARK 465 PHE A 184 REMARK 465 THR A 185 REMARK 465 ASP A 186 REMARK 465 ASN A 187 REMARK 465 GLU B 176 REMARK 465 THR B 177 REMARK 465 THR B 178 REMARK 465 MET B 179 REMARK 465 ARG B 180 REMARK 465 SER B 181 REMARK 465 PRO B 182 REMARK 465 VAL B 183 REMARK 465 PHE B 184 REMARK 465 THR B 185 REMARK 465 ASP B 186 REMARK 465 ASN B 187 REMARK 465 LYS C 220 REMARK 465 GLY C 233 REMARK 465 ARG C 234 REMARK 465 LYS C 235 REMARK 465 LYS D 220 REMARK 465 GLY D 233 REMARK 465 ARG D 234 REMARK 465 LYS D 235 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 OH TYR B 75 NE2 GLN B 80 2.15 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 ARG A 11 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 ARG A 109 NE - CZ - NH2 ANGL. DEV. = 3.3 DEGREES REMARK 500 ARG A 117 NE - CZ - NH1 ANGL. DEV. = -5.2 DEGREES REMARK 500 ARG A 118 CD - NE - CZ ANGL. DEV. = 10.9 DEGREES REMARK 500 ARG A 118 NE - CZ - NH1 ANGL. DEV. = 7.1 DEGREES REMARK 500 ARG A 118 NE - CZ - NH2 ANGL. DEV. = -3.8 DEGREES REMARK 500 ARG A 123 NE - CZ - NH1 ANGL. DEV. = 4.5 DEGREES REMARK 500 ARG A 130 CD - NE - CZ ANGL. DEV. = -8.8 DEGREES REMARK 500 ARG A 130 NE - CZ - NH1 ANGL. DEV. = -8.0 DEGREES REMARK 500 ARG A 130 NE - CZ - NH2 ANGL. DEV. = 8.3 DEGREES REMARK 500 ARG A 155 CD - NE - CZ ANGL. DEV. = 10.7 DEGREES REMARK 500 ARG A 155 NE - CZ - NH2 ANGL. DEV. = -4.0 DEGREES REMARK 500 TYR B 75 CB - CG - CD2 ANGL. DEV. = -3.9 DEGREES REMARK 500 ARG B 109 NE - CZ - NH1 ANGL. DEV. = -3.9 DEGREES REMARK 500 ARG B 109 NE - CZ - NH2 ANGL. DEV. = 5.5 DEGREES REMARK 500 ARG B 130 NE - CZ - NH2 ANGL. DEV. = -6.1 DEGREES REMARK 500 ARG B 155 NE - CZ - NH2 ANGL. DEV. = -4.7 DEGREES REMARK 500 ARG C 228 NE - CZ - NH2 ANGL. DEV. = -4.0 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 THR A 98 -50.30 78.55 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 TRP B 53 -10.39 REMARK 500 VAL B 158 11.38 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 B 300 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 97 SG REMARK 620 2 CYS B 99 SG 89.5 REMARK 620 3 CYS B 145 SG 106.5 115.0 REMARK 620 4 HOH B2098 O 118.6 111.2 113.9 REMARK 620 N 1 2 3 REMARK 630 REMARK 630 MOLECULE TYPE: PEPTIDE-LIKE INHIBITOR REMARK 630 MOLECULE NAME: N-(TERT-BUTOXYCARBONYL)-L-ALPHA-GLUTAMYL-N-[(1R)-1- REMARK 630 (CARBOXYCARBONYL)-3,3-DIFLUOROPROPYL]-L-LEUCINAMIDE REMARK 630 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 630 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 630 REMARK 630 M RES C SSSEQI REMARK 630 2ZF A 401 REMARK 630 2ZF B 401 REMARK 630 SOURCE: NULL REMARK 630 TAXONOMY: NULL REMARK 630 SUBCOMP: BOC GLU LEU FKI REMARK 630 DETAILS: NULL REMARK 700 REMARK 700 SHEET REMARK 700 DETERMINATION METHOD: DSSP REMARK 700 THE SHEETS PRESENTED AS AC AND BC 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 2ZF A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 2ZF B 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 300 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1DXP RELATED DB: PDB REMARK 900 INHIBITION OF THE HEPATITIS C VIRUS NS3/4A PROTEASE. THE CRYSTAL REMARK 900 STRUCTURES OF TWO PROTEASE-INHIBITOR COMPLEXES (APO STRUCTURE) REMARK 900 RELATED ID: 1DY8 RELATED DB: PDB REMARK 900 INHIBITION OF THE HEPATITIS C VIRUS NS3/4A PROTEASE. THE CRYSTAL REMARK 900 STRUCTURES OF TWO PROTEASE-INHIBITOR COMPLEXES (INHIBITOR II) REMARK 900 RELATED ID: 1JXP RELATED DB: PDB REMARK 900 BK STRAIN HEPATITIS C VIRUS (HCV) NS3-NS4A (PROTEASE) REMARK 999 REMARK 999 SEQUENCE REMARK 999 GENOME POLYPROTEIN, ID POLG_HCVJA_7, PROTEASE NS3 REMARK 999 GENOME POLYPROTEIN, ID POLG_HCVJA_8, NONSTRUCTURAL PROTEIN REMARK 999 REMARK 999 THE SWISSPROT ENTRY POLG_HCVJA GIVES A FULL DESCRIPTION OF THE REMARK 999 GENOME POLYPROTEIN FROM HEPATITIS C VIRUS (ISOLATE JAPANESE) REMARK 999 THAT CONTAINS THE FOLLOWING MATURE PROTEINS PRODUCED BY REMARK 999 POST-TRANSLATIONAL PROCESSING - REMARK 999 CAPSID PROTEIN C (CORE PROTEIN) (P22); REMARK 999 ENVELOPE GLYCOPROTEIN E1 (GP32) (GP35); REMARK 999 ENVELOPE GLYCOPROTEIN E2 (GP68) (GP70) (NS1); REMARK 999 PROTEIN P7; REMARK 999 NONSTRUCTURAL PROTEIN NS2 (P21) (EC 3.4.22.*); REMARK 999 PROTEASE/HELICASE NS3 (P70) (EC 3.4.21.*); REMARK 999 NONSTRUCTURAL PROTEIN NS4A (P4); REMARK 999 NONSTRUCTURAL PROTEIN NS4B (P27); REMARK 999 NONSTRUCTURAL PROTEIN NS5A (P56); REMARK 999 NONSTRUCTURAL PROTEIN NS5B (P66) (P70) REMARK 999 (RNA-DIRECTED RNA POLYMERASE) (EC 2.7.7.48)]. REMARK 999 REMARK 999 HOWEVER, THE SWISSPROT ENTRY Q81755 (ISOLATE TAIWANESE) REMARK 999 IS A 100% MATCH TO THE NS3 PROTEIN STUDIED HERE. DBREF 1DY9 A 1 187 UNP Q81755 Q81755 305 491 DBREF 1DY9 B 1 187 UNP Q81755 Q81755 305 491 DBREF 1DY9 C 220 235 UNP Q81755 Q81755 955 970 DBREF 1DY9 D 220 235 UNP Q81755 Q81755 955 970 SEQADV 1DY9 LYS C 220 UNP Q81755 THR 955 ENGINEERED MUTATION SEQADV 1DY9 LYS C 235 UNP Q81755 PRO 970 ENGINEERED MUTATION SEQADV 1DY9 LYS D 220 UNP Q81755 THR 955 ENGINEERED MUTATION SEQADV 1DY9 LYS D 235 UNP Q81755 PRO 970 ENGINEERED MUTATION SEQRES 1 A 187 ALA PRO ILE THR ALA TYR SER GLN GLN THR ARG GLY LEU SEQRES 2 A 187 LEU GLY CYS ILE ILE THR SER LEU THR GLY ARG ASP LYS SEQRES 3 A 187 ASN GLN VAL ASP GLY GLU VAL GLN VAL LEU SER THR ALA SEQRES 4 A 187 THR GLN SER PHE LEU ALA THR CYS VAL ASN GLY VAL CYS SEQRES 5 A 187 TRP THR VAL TYR HIS GLY ALA GLY SER LYS THR LEU ALA SEQRES 6 A 187 GLY PRO LYS GLY PRO ILE THR GLN MET TYR THR ASN VAL SEQRES 7 A 187 ASP GLN ASP LEU VAL GLY TRP PRO ALA PRO PRO GLY ALA SEQRES 8 A 187 ARG SER MET THR PRO CYS THR CYS GLY SER SER ASP LEU SEQRES 9 A 187 TYR LEU VAL THR ARG HIS ALA ASP VAL ILE PRO VAL ARG SEQRES 10 A 187 ARG ARG GLY ASP SER ARG GLY SER LEU LEU SER PRO ARG SEQRES 11 A 187 PRO VAL SER TYR LEU LYS GLY SER SER GLY GLY PRO LEU SEQRES 12 A 187 LEU CYS PRO SER GLY HIS VAL VAL GLY ILE PHE ARG ALA SEQRES 13 A 187 ALA VAL CYS THR ARG GLY VAL ALA LYS ALA VAL ASP PHE SEQRES 14 A 187 ILE PRO VAL GLU SER MET GLU THR THR MET ARG SER PRO SEQRES 15 A 187 VAL PHE THR ASP ASN SEQRES 1 B 187 ALA PRO ILE THR ALA TYR SER GLN GLN THR ARG GLY LEU SEQRES 2 B 187 LEU GLY CYS ILE ILE THR SER LEU THR GLY ARG ASP LYS SEQRES 3 B 187 ASN GLN VAL ASP GLY GLU VAL GLN VAL LEU SER THR ALA SEQRES 4 B 187 THR GLN SER PHE LEU ALA THR CYS VAL ASN GLY VAL CYS SEQRES 5 B 187 TRP THR VAL TYR HIS GLY ALA GLY SER LYS THR LEU ALA SEQRES 6 B 187 GLY PRO LYS GLY PRO ILE THR GLN MET TYR THR ASN VAL SEQRES 7 B 187 ASP GLN ASP LEU VAL GLY TRP PRO ALA PRO PRO GLY ALA SEQRES 8 B 187 ARG SER MET THR PRO CYS THR CYS GLY SER SER ASP LEU SEQRES 9 B 187 TYR LEU VAL THR ARG HIS ALA ASP VAL ILE PRO VAL ARG SEQRES 10 B 187 ARG ARG GLY ASP SER ARG GLY SER LEU LEU SER PRO ARG SEQRES 11 B 187 PRO VAL SER TYR LEU LYS GLY SER SER GLY GLY PRO LEU SEQRES 12 B 187 LEU CYS PRO SER GLY HIS VAL VAL GLY ILE PHE ARG ALA SEQRES 13 B 187 ALA VAL CYS THR ARG GLY VAL ALA LYS ALA VAL ASP PHE SEQRES 14 B 187 ILE PRO VAL GLU SER MET GLU THR THR MET ARG SER PRO SEQRES 15 B 187 VAL PHE THR ASP ASN SEQRES 1 C 16 LYS GLY SER VAL VAL ILE VAL GLY ARG ILE ILE LEU SER SEQRES 2 C 16 GLY ARG LYS SEQRES 1 D 16 LYS GLY SER VAL VAL ILE VAL GLY ARG ILE ILE LEU SER SEQRES 2 D 16 GLY ARG LYS HET 2ZF A 401 35 HET 2ZF B 401 35 HET ZN B 300 1 HETNAM 2ZF N-(TERT-BUTOXYCARBONYL)-L-ALPHA-GLUTAMYL-N-[(1R)-1- HETNAM 2 2ZF (CARBOXYCARBONYL)-3,3-DIFLUOROPROPYL]-L-LEUCINAMIDE HETNAM ZN ZINC ION FORMUL 5 2ZF 2(C21 H33 F2 N3 O9) FORMUL 7 ZN ZN 2+ FORMUL 8 HOH *213(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 LEU A 135 5 3 HELIX 4 4 GLU A 173 MET A 175 5 3 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 VAL B 132 LYS B 136 1 5 SHEET 1 AA 7 THR A 4 GLN A 9 0 SHEET 2 AA 7 VAL C 224 SER C 232 0 SHEET 3 AA 7 VAL A 33 SER A 37 -1 O VAL A 33 N ILE C 229 SHEET 4 AA 7 SER A 42 VAL A 48 -1 O PHE A 43 N LEU 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 PRO 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 2 LEU A 64 GLY A 66 0 SHEET 2 AB 2 GLY A 69 ILE A 71 -1 O GLY A 69 N GLY A 66 SHEET 1 AC 7 ASP A 103 VAL A 107 0 SHEET 2 AC 7 VAL A 113 GLY A 120 -1 O ILE A 114 N LEU A 106 SHEET 3 AC 7 ARG A 123 PRO A 131 -1 O ARG A 123 N ARG A 119 SHEET 4 AC 7 VAL A 163 PRO A 171 -1 O ALA A 164 N ARG A 130 SHEET 5 AC 7 VAL A 150 THR A 160 -1 O ILE A 153 N ILE A 170 SHEET 6 AC 7 PRO A 142 LEU A 144 -1 O LEU A 143 N VAL A 151 SHEET 7 AC 7 ASP A 103 VAL A 107 -1 O TYR A 105 N LEU A 144 SHEET 1 BA 7 ALA B 5 GLN B 9 0 SHEET 2 BA 7 VAL D 224 LEU D 231 -1 O ARG D 228 N GLN B 8 SHEET 3 BA 7 VAL B 33 SER B 37 -1 O VAL B 33 N ILE D 229 SHEET 4 BA 7 SER B 42 VAL B 48 -1 O PHE B 43 N LEU 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 PRO 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 BC 7 ASP B 103 VAL B 107 0 SHEET 2 BC 7 VAL B 113 ARG B 118 -1 O ILE B 114 N LEU B 106 SHEET 3 BC 7 ARG B 123 PRO B 131 -1 O SER B 125 N ARG B 117 SHEET 4 BC 7 VAL B 163 PRO B 171 -1 O ALA B 164 N ARG B 130 SHEET 5 BC 7 VAL B 150 THR B 160 -1 O ILE B 153 N ILE B 170 SHEET 6 BC 7 PRO B 142 LEU B 144 -1 O LEU B 143 N VAL B 151 SHEET 7 BC 7 ASP B 103 VAL B 107 -1 O TYR B 105 N LEU B 144 LINK OG SER A 139 C6 2ZF A 401 1555 1555 1.43 LINK OG SER B 139 C6 2ZF B 401 1555 1555 1.44 LINK SG CYS B 97 ZN ZN B 300 1555 1555 2.66 LINK SG CYS B 99 ZN ZN B 300 1555 1555 2.82 LINK SG CYS B 145 ZN ZN B 300 1555 1555 2.67 LINK ZN ZN B 300 O HOH B2098 1555 1555 2.61 SITE 1 AC1 13 SER A 42 HIS A 57 LYS A 136 GLY A 137 SITE 2 AC1 13 SER A 138 SER A 139 PHE A 154 ARG A 155 SITE 3 AC1 13 ALA A 156 ALA A 157 CYS A 159 HOH A2027 SITE 4 AC1 13 HOH A2098 SITE 1 AC2 13 SER B 42 HIS B 57 VAL B 132 LYS B 136 SITE 2 AC2 13 GLY B 137 SER B 138 SER B 139 PHE B 154 SITE 3 AC2 13 ARG B 155 ALA B 156 ALA B 157 HOH B2102 SITE 4 AC2 13 HOH B2103 SITE 1 AC3 4 CYS B 97 CYS B 99 CYS B 145 HOH B2098 CRYST1 94.350 94.350 82.370 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 0.010599 0.006119 0.000000 0.00000 SCALE2 0.000000 0.012238 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012140 0.00000 MTRIX1 1 0.372400 0.928070 -0.002600 12.21626 1 MTRIX2 1 0.928060 -0.372410 -0.003230 -5.75718 1 MTRIX3 1 -0.003960 -0.001210 -0.999990 14.19541 1