HEADER HYDROLASE 13-JAN-00 1DXP TITLE INHIBITION OF THE HEPATITIS C VIRUS NS3/4A PROTEASE. THE CRYSTAL TITLE 2 STRUCTURES OF TWO PROTEASE-INHIBITOR COMPLEXES (APO STRUCTURE) 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 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HEPATITIS C VIRUS (ISOLATE TAIWAN); SOURCE 3 ORGANISM_TAXID: 31645; SOURCE 4 GENE: HCV; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PT7-7; SOURCE 9 OTHER_DETAILS: CDNA OF HEPATITIS C VIRUS; SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES; SOURCE 12 ORGANISM_SCIENTIFIC: HEPATITIS C VIRUS; SOURCE 13 ORGANISM_TAXID: 31645 KEYWDS SERINE PROTEASE, NS3, NS4A, HEPATITIS C VIRUS, PROTEASE INHIBITION, KEYWDS 2 HYDROLASE 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 9 06-DEC-23 1DXP 1 REMARK LINK REVDAT 8 24-JUL-19 1DXP 1 REMARK REVDAT 7 08-MAY-19 1DXP 1 REMARK REVDAT 6 12-MAR-14 1DXP 1 SOURCE REVDAT 5 13-JUL-11 1DXP 1 VERSN REVDAT 4 24-FEB-09 1DXP 1 VERSN REVDAT 3 25-MAR-04 1DXP 1 JRNL REVDAT 2 28-MAR-02 1DXP 1 JRNL REMARK REVDAT 1 12-JAN-01 1DXP 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. 2.40 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) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 15786 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) : 0.196 REMARK 3 R VALUE (WORKING SET) : 0.198 REMARK 3 FREE R VALUE : 0.298 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 789 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 : 8 REMARK 3 SOLVENT ATOMS : 209 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 45.57 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 46.78 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): 0.410 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.320 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.120 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.140 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) : 0.037 ; 0.040 REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : 0.039 ; 0.050 REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : 0.014 ; 0.020 REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : 0.140 ; 0.150 REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : 0.220 ; 0.300 REMARK 3 MULTIPLE TORSION (A) : 0.300 ; 0.300 REMARK 3 H-BOND (X...Y) (A) : 0.240 ; 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) : 9.000 ; 6.000 REMARK 3 STAGGERED (DEGREES) : 21.600; 15.000 REMARK 3 TRANSVERSE (DEGREES) : 25.000; 20.000 REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 5.570 ; 3.000 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 7.440 ; 5.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 12.140; 6.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 13.970; 8.000 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1DXP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 13-JAN-00. REMARK 100 THE DEPOSITION ID IS D_1290004535. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-APR-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 : EMBL/DESY, HAMBURG REMARK 200 BEAMLINE : X11 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.912 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : BENT MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15786 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 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 (%) : 100.0 REMARK 200 DATA REDUNDANCY : 8.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.07100 REMARK 200 FOR THE DATA SET : 9.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.53 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 5.60 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.36000 REMARK 200 FOR SHELL : 2.200 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 1JXP 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 INCUBATED 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., 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 27.27000 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 54.54000 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 40.90500 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 68.17500 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 13.63500 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: 4140 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10040 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -21.3 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PQS REMARK 350 TOTAL BURIED SURFACE AREA: 4200 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10030 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -21.0 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 A 75 NE2 GLN A 80 2.04 REMARK 500 O ILE A 18 OG1 THR A 22 2.18 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 25 CB - CG - OD2 ANGL. DEV. = 6.5 DEGREES REMARK 500 ARG A 109 C - N - CA ANGL. DEV. = 15.3 DEGREES REMARK 500 ARG A 109 NE - CZ - NH2 ANGL. DEV. = -3.8 DEGREES REMARK 500 ARG A 117 NE - CZ - NH2 ANGL. DEV. = -3.5 DEGREES REMARK 500 ARG A 130 NE - CZ - NH1 ANGL. DEV. = -3.8 DEGREES REMARK 500 ARG A 130 NE - CZ - NH2 ANGL. DEV. = 4.7 DEGREES REMARK 500 VAL A 150 CA - CB - CG2 ANGL. DEV. = -9.4 DEGREES REMARK 500 VAL A 158 CB - CA - C ANGL. DEV. = 12.0 DEGREES REMARK 500 GLN B 28 N - CA - CB ANGL. DEV. = 11.1 DEGREES REMARK 500 ASP B 30 CB - CG - OD1 ANGL. DEV. = 6.5 DEGREES REMARK 500 TYR B 105 CB - CG - CD1 ANGL. DEV. = -3.7 DEGREES REMARK 500 ARG B 109 CD - NE - CZ ANGL. DEV. = -13.3 DEGREES REMARK 500 ARG B 109 NE - CZ - NH1 ANGL. DEV. = -6.6 DEGREES REMARK 500 ARG B 119 CD - NE - CZ ANGL. DEV. = 13.8 DEGREES REMARK 500 ARG B 119 NE - CZ - NH2 ANGL. DEV. = -5.0 DEGREES REMARK 500 ARG B 123 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 ARG B 123 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 TYR B 134 CA - CB - CG ANGL. DEV. = -12.4 DEGREES REMARK 500 ARG C 228 CD - NE - CZ ANGL. DEV. = 9.6 DEGREES REMARK 500 ARG C 228 NE - CZ - NH1 ANGL. DEV. = 4.9 DEGREES REMARK 500 ARG C 228 NE - CZ - NH2 ANGL. DEV. = -7.2 DEGREES REMARK 500 ARG D 228 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 ARG D 228 NE - CZ - NH2 ANGL. DEV. = -5.2 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 38 -155.44 -119.23 REMARK 500 LYS A 68 44.91 -103.81 REMARK 500 ARG A 155 -68.34 -107.00 REMARK 500 THR B 38 -164.06 -117.69 REMARK 500 VAL B 132 -39.54 -36.90 REMARK 500 ARG B 155 -52.43 -120.86 REMARK 500 ARG B 161 33.72 73.38 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 GLY A 60 -13.06 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH B2022 DISTANCE = 6.48 ANGSTROMS REMARK 525 HOH B2027 DISTANCE = 6.17 ANGSTROMS REMARK 525 HOH B2029 DISTANCE = 6.21 ANGSTROMS REMARK 525 HOH C2001 DISTANCE = 6.13 ANGSTROMS 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 A 201 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 97 SG REMARK 620 2 CYS A 99 SG 93.1 REMARK 620 3 CYS A 145 SG 124.4 103.7 REMARK 620 4 HOH A2090 O 114.4 113.7 106.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 201 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 97 SG REMARK 620 2 CYS B 99 SG 101.6 REMARK 620 3 CYS B 145 SG 111.8 113.3 REMARK 620 4 HOH B2106 O 113.2 115.8 101.6 REMARK 620 N 1 2 3 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 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR CHAIN C OF NONSTRUCTURAL REMARK 800 PROTEIN NS4A (P4) REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR CHAIN D OF NONSTRUCTURAL REMARK 800 PROTEIN NS4A (P4) REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1JXP RELATED DB: PDB REMARK 900 BK STRAIN HEPATITIS C VIRUS (HCV) NS3-NS4A (PROTEASE) 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: 1DY9 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 I) 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 1DXP A 1 187 UNP Q81755 Q81755 305 491 DBREF 1DXP B 1 187 UNP Q81755 Q81755 305 491 DBREF 1DXP C 220 235 UNP Q81755 Q81755 955 970 DBREF 1DXP D 220 235 UNP Q81755 Q81755 955 970 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 ZN A 201 1 HET ZN B 201 1 HET GOL B 202 6 HETNAM ZN ZINC ION HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 5 ZN 2(ZN 2+) FORMUL 7 GOL C3 H8 O3 FORMUL 8 HOH *209(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 SER B 133 LEU B 135 5 3 HELIX 8 8 GLU B 173 MET B 175 5 3 SHEET 1 AA 5 VAL A 33 SER A 37 0 SHEET 2 AA 5 SER A 42 VAL A 48 -1 N ALA A 45 O GLN A 34 SHEET 3 AA 5 VAL A 51 VAL A 55 -1 N TRP A 53 O THR A 46 SHEET 4 AA 5 LEU A 82 PRO A 86 -1 N TRP A 85 O CYS A 52 SHEET 5 AA 5 TYR A 75 ASN A 77 -1 N ASN A 77 O LEU A 82 SHEET 1 AB 7 VAL A 113 ARG A 117 0 SHEET 2 AB 7 ASP A 103 VAL A 107 -1 N LEU A 106 O ILE A 114 SHEET 3 AB 7 PRO A 142 CYS A 145 -1 N LEU A 144 O TYR A 105 SHEET 4 AB 7 VAL A 150 VAL A 158 -1 N GLY A 152 O LEU A 143 SHEET 5 AB 7 ALA A 166 PRO A 171 -1 N ILE A 170 O ILE A 153 SHEET 6 AB 7 ARG A 123 LEU A 126 -1 N GLY A 124 O VAL A 167 SHEET 7 AB 7 VAL A 116 ARG A 118 -1 N ARG A 117 O SER A 125 SHEET 1 BA 5 VAL B 33 SER B 37 0 SHEET 2 BA 5 SER B 42 VAL B 48 -1 N ALA B 45 O GLN B 34 SHEET 3 BA 5 VAL B 51 VAL B 55 -1 N TRP B 53 O THR B 46 SHEET 4 BA 5 LEU B 82 PRO B 86 -1 N TRP B 85 O CYS B 52 SHEET 5 BA 5 TYR B 75 ASN B 77 -1 N ASN B 77 O LEU B 82 SHEET 1 BB 7 VAL B 113 ARG B 117 0 SHEET 2 BB 7 ASP B 103 VAL B 107 -1 N LEU B 106 O ILE B 114 SHEET 3 BB 7 PRO B 142 CYS B 145 -1 N LEU B 144 O TYR B 105 SHEET 4 BB 7 VAL B 150 VAL B 158 -1 N GLY B 152 O LEU B 143 SHEET 5 BB 7 ALA B 166 PRO B 171 -1 N ILE B 170 O ILE B 153 SHEET 6 BB 7 ARG B 123 LEU B 126 -1 N GLY B 124 O VAL B 167 SHEET 7 BB 7 VAL B 116 ARG B 118 -1 N ARG B 117 O SER B 125 LINK SG CYS A 97 ZN ZN A 201 1555 1555 2.62 LINK SG CYS A 99 ZN ZN A 201 1555 1555 2.64 LINK SG CYS A 145 ZN ZN A 201 1555 1555 2.69 LINK ZN ZN A 201 O HOH A2090 1555 1555 2.60 LINK SG CYS B 97 ZN ZN B 201 1555 1555 2.49 LINK SG CYS B 99 ZN ZN B 201 1555 1555 2.65 LINK SG CYS B 145 ZN ZN B 201 1555 1555 2.60 LINK ZN ZN B 201 O HOH B2106 1555 1555 2.41 SITE 1 AC1 4 CYS A 97 CYS A 99 CYS A 145 HOH A2090 SITE 1 AC2 4 CYS B 97 CYS B 99 CYS B 145 HOH B2106 SITE 1 AC3 5 SER B 42 LYS B 136 GLY B 137 SER B 138 SITE 2 AC3 5 SER B 139 SITE 1 AC4 36 ILE A 3 THR A 4 ALA A 5 TYR A 6 SITE 2 AC4 36 SER A 7 GLN A 8 GLN A 9 THR A 10 SITE 3 AC4 36 ARG A 11 SER A 20 GLN A 28 ASP A 30 SITE 4 AC4 36 GLY A 31 GLU A 32 VAL A 33 GLN A 34 SITE 5 AC4 36 VAL A 35 LEU A 36 SER A 37 THR A 38 SITE 6 AC4 36 LYS A 62 THR A 63 LEU A 64 ALA A 65 SITE 7 AC4 36 PRO A 70 MET A 94 THR A 108 ARG A 109 SITE 8 AC4 36 LEU A 144 HOH A2024 HOH A2045 HOH C2006 SITE 9 AC4 36 HOH C2007 HOH C2008 HOH C2009 HOH C2011 SITE 1 AC5 30 THR B 4 ALA B 5 TYR B 6 SER B 7 SITE 2 AC5 30 GLN B 8 GLN B 9 THR B 10 CYS B 16 SITE 3 AC5 30 THR B 19 SER B 20 GLN B 28 ASP B 30 SITE 4 AC5 30 GLY B 31 GLU B 32 VAL B 33 GLN B 34 SITE 5 AC5 30 VAL B 35 LEU B 36 SER B 37 LYS B 62 SITE 6 AC5 30 THR B 63 LEU B 64 ALA B 65 PRO B 70 SITE 7 AC5 30 ARG B 92 THR B 108 ARG B 109 HOH B2042 SITE 8 AC5 30 HOH B2071 HOH D2002 CRYST1 92.980 92.980 81.810 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 0.010755 0.006209 0.000000 0.00000 SCALE2 0.000000 0.012419 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012223 0.00000 MTRIX1 1 0.371280 -0.928520 -0.000390 57.71175 1 MTRIX2 1 -0.928500 -0.371260 -0.007730 73.00011 1 MTRIX3 1 0.007030 0.003230 -0.999970 -0.38373 1