10 20 30 40 50 60 70 80 2WCX - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER HYDROLASE 17-MAR-09 2WCX
TITLE CRYSTAL STRUCTURE OF HEPATITIS C VIRUS NS5B POLYMERASE IN TITLE 2 COMPLEX WITH THIENOPYRROLE-BASED FINGER-LOOP INHIBITORS
COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA-DIRECTED RNA POLYMERASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: NS5B, RESIDUES 2420-2955; COMPND 5 SYNONYM: HEPATITIS C VIRUS RNA-DEPENDENT-RNA-POLYMERASE, COMPND 6 NS5B, P68; COMPND 7 EC: 2.7.7.48; COMPND 8 ENGINEERED: YES
SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HEPATITIS C VIRUS; SOURCE 3 ORGANISM_TAXID: 11105; SOURCE 4 STRAIN: (ISOLATE BK); SOURCE 5 VARIANT: GENOTYPE 1B; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR: T7; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PT7.7; SOURCE 11 OTHER_DETAILS: GENBANK ACCESSION NUMBER AB016785
KEYWDS ENVELOPE PROTEIN, HEPATITIS C VIRUS, RNA-DEPENDENT RNA-POLYMERASE, KEYWDS 2 NUCLEOTIDE-BINDING, ALLOSTERIC INHIBITOR, NON NUCLEOSIDE INHIBITOR, KEYWDS 3 NNI, HCV, NS5B, MEMBRANE, HELICASE, HYDROLASE, POLYMERASE, KEYWDS 4 ATP-BINDING, RNA-BINDING, GENOTYPE 1B, VIRAL PROTEIN, KEYWDS 5 TRANSMEMBRANE, RNA REPLICATION
EXPDTA X-RAY DIFFRACTION
AUTHOR S.DI MARCO
REVDAT 3 23-NOV-11 2WCX 1 KEYWDS JRNL REMARK FORMUL REVDAT 3 2 ATOM VERSN REVDAT 2 08-SEP-09 2WCX 1 JRNL REVDAT 1 18-AUG-09 2WCX 0
JRNL AUTH J.I.MARTIN HERNANDO,J.M.ONTORIA,S.MALANCONA,B.ATTENNI, JRNL AUTH 2 F.FIORE,F.BONELLI,U.KOCH,S.DI MARCO,S.COLARUSSO,S.PONZI, JRNL AUTH 3 N.GENNARI,S.E.VIGNETTI,M.DEL ROSARIO RICO FERREIRA, JRNL AUTH 4 J.HABERMANN,M.ROWLEY,F.NARJES JRNL TITL OPTIMIZATION OF THIENOPYRROLE-BASED FINGER-LOOP INHIBITORS JRNL TITL 2 OF THE HEPATITIS C VIRUS NS5B POLYMERASE. JRNL REF CHEMMEDCHEM V. 4 1695 2009 JRNL REFN ISSN 1860-7179 JRNL PMID 19672916 JRNL DOI 10.1002/CMDC.200900184
REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH S.DI MARCO,C.VOLPARI,L.TOMEI,S.ALTAMURA,S.HARPER, REMARK 1 AUTH 2 F.NARJES,U.KOCH,M.ROWLEY,R.DE FRANCESCO, REMARK 1 AUTH 3 G.MIGLIACCIO,A.CARFI REMARK 1 TITL INTERDOMAIN COMMUNICATION IN HEPATITIS C VIRUS REMARK 1 TITL 2 POLYMERASE ABOLISHED BY SMALL MOLECULE INHIBITORS REMARK 1 TITL 3 BOUND TO A NOVEL ALLOSTERIC SITE. REMARK 1 REF J.BIOL.CHEM. V. 280 29765 2005 REMARK 1 REFN ISSN 0021-9258 REMARK 1 PMID 15955819 REMARK 1 DOI 10.1074/JBC.M505423200
REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.0 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 95.35 REMARK 3 DATA CUTOFF (SIGMA(F)) : NONE REMARK 3 COMPLETENESS FOR RANGE (%) : 96.83 REMARK 3 NUMBER OF REFLECTIONS : 39241 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) : 0.16931 REMARK 3 R VALUE (WORKING SET) : 0.16717 REMARK 3 FREE R VALUE : 0.20920 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.1 REMARK 3 FREE R VALUE TEST SET COUNT : 2088 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) : 2.000 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.052 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2768 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.178 REMARK 3 BIN FREE R VALUE SET COUNT : 138 REMARK 3 BIN FREE R VALUE : 0.247 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3978 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 26 REMARK 3 SOLVENT ATOMS : 507 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 21.65 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.471 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.08 REMARK 3 B22 (A**2) : -0.21 REMARK 3 B33 (A**2) : 0.30 REMARK 3 B12 (A**2) : 0.00 REMARK 3 B13 (A**2) : 0.00 REMARK 3 B23 (A**2) : 0.00 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): 0.146 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.146 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.099 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.954 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.926 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4086 ; 0.022 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 3717 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5541 ; 1.909 ; 1.963 REMARK 3 BOND ANGLES OTHERS (DEGREES): 8647 ; 1.670 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 509 ; 4.639 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 753 ;18.594 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 626 ; 0.125 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4494 ; 0.009 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 827 ; 0.003 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 998 ; 0.252 ; 0.300 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 3855 ; 0.321 ; 0.300 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): 4 ; 1.250 ; 0.500 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 476 ; 0.229 ; 0.500 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): 17 ; 0.217 ; 0.300 REMARK 3 SYMMETRY VDW OTHERS (A): 34 ; 0.254 ; 0.300 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 36 ; 0.829 ; 0.500 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): 2554 ; 1.196 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4126 ; 2.233 ; 2.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1532 ; 3.509 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1415 ; 5.681 ; 4.500 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 : 1.40 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 REMARK 3 RIDING POSITIONS. NO ELECTRON DENSITY WAS PRESENT FOR REMARK 3 RESIDUES 22-35, 148-152 AND 532-536 WHICH WERE THEREFORE REMARK 3 EXCLUDED FROM THE REFINEMENT. IN ADDITION, SIDE CHAIN DENSITY REMARK 3 FOR RESIDUES GLU18, LYS20 AND LEU21 WAS MISSING AND REMARK 3 THEREFORE THESE RESIDUES HAVE BEEN MODELED AS ALANINE.
REMARK 4 REMARK 4 2WCX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 18-MAR-09. REMARK 100 THE PDBE ID CODE IS EBI-39096.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.931 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 42683 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.00 REMARK 200 RESOLUTION RANGE LOW (A) : 33.71 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.0 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.2 REMARK 200 DATA REDUNDANCY : 6.9 REMARK 200 R MERGE (I) : 0.09 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 18.00 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.11 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.9 REMARK 200 DATA REDUNDANCY IN SHELL : 6.2 REMARK 200 R MERGE FOR SHELL (I) : 0.35 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 5.20 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 1CSJ REMARK 200 REMARK 200 REMARK: NONE
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.41 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.45 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL
REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X+1/2,Y+1/2,-Z REMARK 290 4555 X+1/2,-Y+1/2,-Z 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 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 34.20350 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 47.35400 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 34.20350 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 47.35400 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 MET A 0 REMARK 465 PRO A 22 REMARK 465 ILE A 23 REMARK 465 ASN A 24 REMARK 465 ALA A 25 REMARK 465 LEU A 26 REMARK 465 SER A 27 REMARK 465 ASN A 28 REMARK 465 SER A 29 REMARK 465 LEU A 30 REMARK 465 LEU A 31 REMARK 465 ARG A 32 REMARK 465 HIS A 33 REMARK 465 HIS A 34 REMARK 465 ASN A 35 REMARK 465 GLN A 148 REMARK 465 PRO A 149 REMARK 465 GLU A 150 REMARK 465 LYS A 151 REMARK 465 GLY A 152 REMARK 465 THR A 532 REMARK 465 LYS A 533 REMARK 465 LEU A 534 REMARK 465 LYS A 535 REMARK 465 LEU A 536
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 GLU A 18 CG CD OE1 OE2 REMARK 470 LYS A 20 CG CD CE NZ REMARK 470 LEU A 21 CG CD1 CD2 REMARK 470 HIS A 402 CG ND1 CD2 CE1 NE2
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 177 O HOH A 2224 2.12 REMARK 500 NE2 GLN A 184 OE1 GLN A 194 2.13 REMARK 500 NH1 ARG A 234 OE2 GLU A 258 2.14 REMARK 500 CE A MET A 414 O HOH A 2442 1.97 REMARK 500 OE1 GLU A 455 O HOH A 2446 1.80 REMARK 500 OG SER A 478 O HOH A 2470 1.87 REMARK 500 OD1A ASN A 483 O HOH A 2474 1.82 REMARK 500 ND2A ASN A 483 O HOH A 2476 2.18 REMARK 500 O HOH A 2022 O HOH A 2287 1.97 REMARK 500 O HOH A 2047 O HOH A 2210 1.47 REMARK 500 O HOH A 2048 O HOH A 2505 1.67 REMARK 500 O HOH A 2067 O HOH A 2167 2.12 REMARK 500 O HOH A 2151 O HOH A 2154 2.06 REMARK 500 O HOH A 2212 O HOH A 2213 2.06 REMARK 500 O HOH A 2221 O HOH A 2224 1.55 REMARK 500 O HOH A 2243 O HOH A 2245 1.71 REMARK 500 O HOH A 2335 O HOH A 2336 1.72 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 OD1B ASN A 483 OD1B ASN A 483 2655 1.51 REMARK 500 O HOH A 2108 O HOH A 2108 2665 0.52 REMARK 500 O HOH A 2112 O HOH A 2112 2665 0.77 REMARK 500 O HOH A 2138 O HOH A 2138 2665 0.90 REMARK 500 O HOH A 2158 O HOH A 2158 2565 1.58 REMARK 500 O HOH A 2159 O HOH A 2159 2565 1.71 REMARK 500 O HOH A 2221 O HOH A 2221 2665 0.54 REMARK 500 O HOH A 2221 O HOH A 2224 2665 1.73 REMARK 500 O HOH A 2258 O HOH A 2258 2655 1.69 REMARK 500 O HOH A 2477 O HOH A 2477 2655 1.62 REMARK 500 REMARK 500 REMARK: NULL 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 LYS A 81 CE LYS A 81 NZ 0.186 REMARK 500 GLU A 237 CD GLU A 237 OE1 0.093 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 62 CB - CG - OD2 ANGL. DEV. = 5.4 DEGREES REMARK 500 ASP A 135 CB - CG - OD2 ANGL. DEV. = 6.0 DEGREES REMARK 500 ASP A 177 CB - CG - OD2 ANGL. DEV. = 5.6 DEGREES REMARK 500 CYS A 274 CB - CA - C ANGL. DEV. = -11.0 DEGREES REMARK 500 ARG A 465 NE - CZ - NH1 ANGL. DEV. = -3.7 DEGREES REMARK 500 ARG A 490 NE - CZ - NH2 ANGL. DEV. = -3.6 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 VAL A 131 -35.33 -134.08 REMARK 500 LEU A 260 -55.56 -123.90 REMARK 500 SER A 347 -1.05 108.06 REMARK 500 ARG A 401 -106.11 -104.95 REMARK 500 HIS A 402 141.50 139.97 REMARK 500 TYR A 448 43.42 38.56 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 MN A1532 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 221 O REMARK 620 2 HOH A2504 O 94.4 REMARK 620 3 HOH A2505 O 88.9 62.6 REMARK 620 4 ASP A 220 OD2 89.7 92.3 154.7 REMARK 620 5 ASP A 318 OD2 93.8 167.4 108.1 97.2 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A1533 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 220 OD1 REMARK 620 2 HOH A2507 O 93.7 REMARK 620 3 ASP A 318 OD1 94.2 164.0 REMARK 620 4 ASP A 319 OD1 96.3 95.7 97.2 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 MN A1532 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A1533 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE VGC A1534
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1NHU RELATED DB: PDB REMARK 900 HEPATITIS C VIRUS RNA POLYMERASE IN COMPLEX REMARK 900 WITH NON-NUCLEOSIDE ANALOGUE INHIBITOR REMARK 900 RELATED ID: 2I1R RELATED DB: PDB REMARK 900 NOVEL THIAZOLONES AS HCV NS5B POLYMERASE REMARK 900 INHIBITORS:FURTHER DESIGNS, SYNTHESIS, SAR AND REMARK 900 X-RAY COMPLEX STRUCTURE REMARK 900 RELATED ID: 1JXP RELATED DB: PDB REMARK 900 BK STRAIN HEPATITIS C VIRUS (HCV) NS3-NS4A REMARK 900 RELATED ID: 2JC1 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HEPATITIS C VIRUS REMARK 900 POLYMERASE IN COMPLEX WITH INHIBITOR SB698223 REMARK 900 RELATED ID: 1GX6 RELATED DB: PDB REMARK 900 HEPATITIS C VIRUS RNA POLYMERASE IN COMPLEX REMARK 900 WITH UTP AND MANGANESE REMARK 900 RELATED ID: 1A1Q RELATED DB: PDB REMARK 900 HEPATITIS C VIRUS NS3 PROTEINASE REMARK 900 RELATED ID: 1C2P RELATED DB: PDB REMARK 900 HEPATITIS C VIRUS NS5B RIBONUCLEIC ACID- REMARK 900 DEPENDENT RIBONUCLEIC ACID POLYMERASE REMARK 900 RELATED ID: 1CU1 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF AN ENZYME COMPLEX FROM REMARK 900 HEPATITIS C VIRUS REMARK 900 RELATED ID: 1NS3 RELATED DB: PDB REMARK 900 STRUCTURE OF HCV PROTEASE (BK STRAIN) REMARK 900 RELATED ID: 2JC0 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HEPATITIS C VIRUS REMARK 900 POLYMERASE IN COMPLEX WITH INHIBITOR SB655264 REMARK 900 RELATED ID: 2AX1 RELATED DB: PDB REMARK 900 HEPATITIS C VIRUS NS5B RNA POLYMERASE IN REMARK 900 COMPLEX WITH ACOVALENT INHIBITOR (5EE) REMARK 900 RELATED ID: 1NHV RELATED DB: PDB REMARK 900 HEPATITIS C VIRUS RNA POLYMERASE IN COMPLEX REMARK 900 WITH NON-NUCLEOSIDE ANALOGUE INHIBITOR REMARK 900 RELATED ID: 1CSJ RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE RIBONUCLEIC ACID- REMARK 900 DEPENDENT RIBONUCLEIC ACID POLYMERASE OF REMARK 900 HEPATITIS C VIRUS REMARK 900 RELATED ID: 2BRL RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HEPATITIS C VIRUS REMARK 900 POLYMERASE IN COMPLEX WITH AN ALLOSTERIC REMARK 900 INHIBITOR (COMPOUND 2) REMARK 900 RELATED ID: 2BRK RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HEPATITIS C VIRUS REMARK 900 POLYMERASE IN COMPLEX WITH AN ALLOSTERIC REMARK 900 INHIBITOR (COMPOUND 1) REMARK 900 RELATED ID: 1GX5 RELATED DB: PDB REMARK 900 HEPATITIS C VIRUS RNA POLYMERASE IN COMPLEX REMARK 900 WITH GTP AND MANGANESE REMARK 900 RELATED ID: 2AX0 RELATED DB: PDB REMARK 900 HEPATITIS C VIRUS NS5B RNA POLYMERASE IN REMARK 900 COMPLEX WITH ACOVALENT INHIBITOR (5X) REMARK 900 RELATED ID: 2AWZ RELATED DB: PDB REMARK 900 HEPATITIS C VIRUS NS5B RNA POLYMERASE IN REMARK 900 COMPLEX WITH ACOVALENT INHIBITOR (5H) REMARK 900 RELATED ID: 1QUV RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE RIBONUCLEIC ACID REMARK 900 DIRECTED RIBONUCLEIC ACID POLYMERASE OF REMARK 900 HEPATITIS C VIRUS REMARK 900 RELATED ID: 1OS5 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HCV NS5B RNA POLYMERASE REMARK 900 COMPLEXED WITHA NOVEL NON-COMPETITIVE REMARK 900 INHIBITOR.
REMARK 999 REMARK 999 SEQUENCE REMARK 999 NS5B PROTEIN, GENOTYPE 1B AND STRAIN BK, LACKING THE C- REMARK 999 TERMINAL 55 AMINO ACIDS. TOTAL AMINO ACIDS 535, UNIPROT REMARK 999 REFERENCE P26663, 2420-2955
DBREF 2WCX A 0 0 PDB 2WCX 2WCX 0 0 DBREF 2WCX A 1 536 UNP P26663 POLG_HCVBK 2420 2955
SEQRES 1 A 537 MET SER MET SER TYR THR TRP THR GLY ALA LEU ILE THR SEQRES 2 A 537 PRO CYS ALA ALA GLU GLU SER LYS LEU PRO ILE ASN ALA SEQRES 3 A 537 LEU SER ASN SER LEU LEU ARG HIS HIS ASN MET VAL TYR SEQRES 4 A 537 ALA THR THR SER ARG SER ALA GLY LEU ARG GLN LYS LYS SEQRES 5 A 537 VAL THR PHE ASP ARG LEU GLN VAL LEU ASP ASP HIS TYR SEQRES 6 A 537 ARG ASP VAL LEU LYS GLU MET LYS ALA LYS ALA SER THR SEQRES 7 A 537 VAL LYS ALA LYS LEU LEU SER VAL GLU GLU ALA CYS LYS SEQRES 8 A 537 LEU THR PRO PRO HIS SER ALA LYS SER LYS PHE GLY TYR SEQRES 9 A 537 GLY ALA LYS ASP VAL ARG ASN LEU SER SER LYS ALA VAL SEQRES 10 A 537 ASN HIS ILE HIS SER VAL TRP LYS ASP LEU LEU GLU ASP SEQRES 11 A 537 THR VAL THR PRO ILE ASP THR THR ILE MET ALA LYS ASN SEQRES 12 A 537 GLU VAL PHE CYS VAL GLN PRO GLU LYS GLY GLY ARG LYS SEQRES 13 A 537 PRO ALA ARG LEU ILE VAL PHE PRO ASP LEU GLY VAL ARG SEQRES 14 A 537 VAL CYS GLU LYS MET ALA LEU TYR ASP VAL VAL SER THR SEQRES 15 A 537 LEU PRO GLN VAL VAL MET GLY SER SER TYR GLY PHE GLN SEQRES 16 A 537 TYR SER PRO GLY GLN ARG VAL GLU PHE LEU VAL ASN THR SEQRES 17 A 537 TRP LYS SER LYS LYS ASN PRO MET GLY PHE SER TYR ASP SEQRES 18 A 537 THR ARG CYS PHE ASP SER THR VAL THR GLU ASN ASP ILE SEQRES 19 A 537 ARG VAL GLU GLU SER ILE TYR GLN CYS CYS ASP LEU ALA SEQRES 20 A 537 PRO GLU ALA ARG GLN ALA ILE LYS SER LEU THR GLU ARG SEQRES 21 A 537 LEU TYR ILE GLY GLY PRO LEU THR ASN SER LYS GLY GLN SEQRES 22 A 537 ASN CYS GLY TYR ARG ARG CYS ARG ALA SER GLY VAL LEU SEQRES 23 A 537 THR THR SER CYS GLY ASN THR LEU THR CYS TYR LEU LYS SEQRES 24 A 537 ALA SER ALA ALA CYS ARG ALA ALA LYS LEU GLN ASP CYS SEQRES 25 A 537 THR MET LEU VAL ASN GLY ASP ASP LEU VAL VAL ILE CYS SEQRES 26 A 537 GLU SER ALA GLY THR GLN GLU ASP ALA ALA SER LEU ARG SEQRES 27 A 537 VAL PHE THR GLU ALA MET THR ARG TYR SER ALA PRO PRO SEQRES 28 A 537 GLY ASP PRO PRO GLN PRO GLU TYR ASP LEU GLU LEU ILE SEQRES 29 A 537 THR SER CYS SER SER ASN VAL SER VAL ALA HIS ASP ALA SEQRES 30 A 537 SER GLY LYS ARG VAL TYR TYR LEU THR ARG ASP PRO THR SEQRES 31 A 537 THR PRO LEU ALA ARG ALA ALA TRP GLU THR ALA ARG HIS SEQRES 32 A 537 THR PRO VAL ASN SER TRP LEU GLY ASN ILE ILE MET TYR SEQRES 33 A 537 ALA PRO THR LEU TRP ALA ARG MET ILE LEU MET THR HIS SEQRES 34 A 537 PHE PHE SER ILE LEU LEU ALA GLN GLU GLN LEU GLU LYS SEQRES 35 A 537 ALA LEU ASP CYS GLN ILE TYR GLY ALA CYS TYR SER ILE SEQRES 36 A 537 GLU PRO LEU ASP LEU PRO GLN ILE ILE GLU ARG LEU HIS SEQRES 37 A 537 GLY LEU SER ALA PHE SER LEU HIS SER TYR SER PRO GLY SEQRES 38 A 537 GLU ILE ASN ARG VAL ALA SER CYS LEU ARG LYS LEU GLY SEQRES 39 A 537 VAL PRO PRO LEU ARG VAL TRP ARG HIS ARG ALA ARG SER SEQRES 40 A 537 VAL ARG ALA ARG LEU LEU SER GLN GLY GLY ARG ALA ALA SEQRES 41 A 537 THR CYS GLY LYS TYR LEU PHE ASN TRP ALA VAL LYS THR SEQRES 42 A 537 LYS LEU LYS LEU
HET MN A1532 1 HET MN A1533 1 HET VGC A1534 24
HETNAM MN MANGANESE (II) ION HETNAM VGC 6-CYCLOHEXYL-4-METHYL-5-PHENYL-4H-THIENO[3,2- HETNAM 2 VGC B]PYRROLE-2-CARBOXYLIC ACID
FORMUL 2 MN 2(MN 2+) FORMUL 3 VGC C20 H21 N O2 S FORMUL 4 HOH *507(H2 O)
HELIX 1 1 THR A 41 ARG A 43 5 3 HELIX 2 2 SER A 44 THR A 53 1 10 HELIX 3 3 ASP A 61 SER A 76 1 16 HELIX 4 4 SER A 84 LEU A 91 1 8 HELIX 5 5 GLY A 104 ASN A 110 1 7 HELIX 6 6 SER A 112 ASP A 129 1 18 HELIX 7 7 ASP A 164 GLY A 188 1 25 HELIX 8 8 GLY A 192 TYR A 195 5 4 HELIX 9 9 SER A 196 SER A 210 1 15 HELIX 10 10 CYS A 223 VAL A 228 1 6 HELIX 11 11 THR A 229 GLN A 241 1 13 HELIX 12 12 ALA A 246 LEU A 260 1 15 HELIX 13 13 THR A 286 ALA A 306 1 21 HELIX 14 14 GLY A 328 TYR A 346 1 19 HELIX 15 15 ASP A 359 ILE A 363 5 5 HELIX 16 16 PRO A 388 ARG A 401 1 14 HELIX 17 17 ASN A 406 TYR A 415 1 10 HELIX 18 18 THR A 418 ILE A 424 1 7 HELIX 19 19 ILE A 424 GLU A 437 1 14 HELIX 20 20 GLU A 455 LEU A 457 5 3 HELIX 21 21 ASP A 458 GLY A 468 1 11 HELIX 22 22 LEU A 469 SER A 473 5 5 HELIX 23 23 SER A 478 GLY A 493 1 16 HELIX 24 24 PRO A 496 GLN A 514 1 19 HELIX 25 25 GLY A 515 PHE A 526 1 12 HELIX 26 26 ASN A 527 VAL A 530 5 4
SHEET 1 AA 5 TYR A 4 TRP A 6 0 SHEET 2 AA 5 ASN A 273 ARG A 277 -1 O TYR A 276 N THR A 5 SHEET 3 AA 5 GLY A 264 THR A 267 -1 O GLY A 264 N ARG A 277 SHEET 4 AA 5 THR A 136 ALA A 140 1 O THR A 136 N THR A 267 SHEET 5 AA 5 LEU A 159 PHE A 162 -1 O ILE A 160 N MET A 139 SHEET 1 AB 2 VAL A 37 ALA A 39 0 SHEET 2 AB 2 VAL A 144 CYS A 146 -1 O PHE A 145 N TYR A 38 SHEET 1 AC 3 PRO A 214 ASP A 220 0 SHEET 2 AC 3 ASP A 319 GLU A 325 -1 O LEU A 320 N TYR A 219 SHEET 3 AC 3 GLN A 309 ASN A 316 -1 O GLN A 309 N GLU A 325 SHEET 1 AD 2 ASN A 369 HIS A 374 0 SHEET 2 AD 2 ARG A 380 THR A 385 -1 O VAL A 381 N ALA A 373 SHEET 1 AE 2 LEU A 443 ILE A 447 0 SHEET 2 AE 2 ALA A 450 ILE A 454 -1 O ALA A 450 N ILE A 447
LINK MN MN A1532 O THR A 221 1555 1555 2.15 LINK MN MN A1532 O HOH A2504 1555 1555 2.38 LINK MN MN A1532 O HOH A2505 1555 1555 2.37 LINK MN MN A1532 OD2 ASP A 220 1555 1555 2.12 LINK MN MN A1532 OD2 ASP A 318 1555 1555 2.11 LINK MN MN A1533 O HOH A2507 1555 1555 2.22 LINK MN MN A1533 OD1 ASP A 318 1555 1555 2.05 LINK MN MN A1533 OD1 ASP A 319 1555 1555 2.19 LINK MN MN A1533 OD1 ASP A 220 1555 1555 2.15
SITE 1 AC1 6 ASP A 220 THR A 221 ASP A 318 MN A1533 SITE 2 AC1 6 HOH A2504 HOH A2505 SITE 1 AC2 5 ASP A 220 ASP A 318 ASP A 319 MN A1532 SITE 2 AC2 5 HOH A2507 SITE 1 AC3 10 VAL A 37 LEU A 392 ALA A 393 HIS A 428 SITE 2 AC3 10 LEU A 492 VAL A 494 PRO A 495 ARG A 503 SITE 3 AC3 10 HOH A2487 HOH A2497
CRYST1 68.407 94.708 95.540 90.00 90.00 90.00 P 21 21 2 4
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 0.014618 0.000000 0.000000 0.00000
SCALE2 0.000000 0.010559 0.000000 0.00000
SCALE3 0.000000 0.000000 0.010467 0.00000