HEADER TRANSFERASE 06-MAY-05 2BRL TITLE CRYSTAL STRUCTURE OF HEPATITIS C VIRUS POLYMERASE IN COMPLEX WITH AN TITLE 2 ALLOSTERIC INHIBITOR (COMPOUND 2) COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA-DIRECTED RNA POLYMERASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: NS5B CATALYTIC DOMAIN, RESIDUES 2420-2955; COMPND 5 SYNONYM: HEPATITIS C VIRUS POLYMERASE, P68, NS5B; COMPND 6 EC: 2.7.7.48; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HEPATITIS C VIRUS; SOURCE 3 ORGANISM_COMMON: HCV; SOURCE 4 ORGANISM_TAXID: 11103; SOURCE 5 STRAIN: GENOTYPE 1B, STRAIN BK; 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 TRANSFERASE, HEPATITIS C VIRUS, HCV, NS5B, POLYMERASE, RNA-DEPENDENT KEYWDS 2 RNA- POLYMERASE, ALLOSTERIC INHIBITOR, NUCLEOTIDYLTRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR S.DI MARCO,C.VOLPARI,A.CARFI REVDAT 3 13-DEC-23 2BRL 1 LINK REVDAT 2 24-FEB-09 2BRL 1 VERSN REVDAT 1 14-JUN-05 2BRL 0 JRNL AUTH S.DI MARCO,C.VOLPARI,L.TOMEI,S.ALTAMURA,S.HARPER,F.NARJES, JRNL AUTH 2 U.KOCH,M.ROWLEY,R.DE FRANCESCO,G.MIGLIACCIO,A.CARFI JRNL TITL INTERDOMAIN COMMUNICATION IN HEPATITIS C VIRUS POLYMERASE JRNL TITL 2 ABOLISHED BY SMALL-MOLECULE INHIBITORS BOUND TO A NOVEL JRNL TITL 3 ALLOSTERIC SITE JRNL REF J.BIOL.CHEM. V. 280 29765 2005 JRNL REFN ISSN 0021-9258 JRNL PMID 15955819 JRNL DOI 10.1074/JBC.M505423200 REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.1.24 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 23759 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) : 0.193 REMARK 3 R VALUE (WORKING SET) : 0.189 REMARK 3 FREE R VALUE : 0.255 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1279 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) : 2.40 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.46 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1715 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.1850 REMARK 3 BIN FREE R VALUE SET COUNT : 89 REMARK 3 BIN FREE R VALUE : 0.2670 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3968 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 39 REMARK 3 SOLVENT ATOMS : 354 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 33.72 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.89000 REMARK 3 B22 (A**2) : -2.94000 REMARK 3 B33 (A**2) : 1.05000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.385 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.267 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.175 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 7.265 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.941 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.895 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4095 ; 0.015 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 3717 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5554 ; 1.496 ; 1.966 REMARK 3 BOND ANGLES OTHERS (DEGREES): 8641 ; 1.178 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 509 ; 6.176 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 629 ; 0.080 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4497 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 827 ; 0.002 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 874 ; 0.209 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 4361 ; 0.236 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): 2387 ; 0.098 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 204 ; 0.205 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 16 ; 0.303 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 44 ; 0.304 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 14 ; 0.336 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 2554 ; 0.753 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4123 ; 1.470 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1541 ; 2.244 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1431 ; 3.913 ; 4.500 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 : 1.40 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 RIDING REMARK 3 POSITIONS. REMARK 4 REMARK 4 2BRL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 06-MAY-05. REMARK 100 THE DEPOSITION ID IS D_1290023939. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-JUL-03 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 6.00 REMARK 200 NUMBER OF CRYSTALS USED : 4 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) : 0.9340 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25135 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 5.200 REMARK 200 R MERGE (I) : 0.08000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.0000 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 (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 5.00 REMARK 200 R MERGE FOR SHELL (I) : 0.32000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.300 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: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.93 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.61 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 6.00 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 34.15150 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 47.42700 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 34.15150 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 47.42700 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: PQS 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 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 2135 2.11 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 O HOH A 2067 O HOH A 2067 2665 1.85 REMARK 500 OD1 ASN A 483 OD1 ASN A 483 2655 2.01 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 387 CB - CG - OD2 ANGL. DEV. = 5.5 DEGREES REMARK 500 MET A 414 CA - CB - CG ANGL. DEV. = 18.8 DEGREES REMARK 500 MET A 414 CA - CB - CG ANGL. DEV. = -11.8 DEGREES REMARK 500 ASP A 458 CB - CG - OD2 ANGL. DEV. = 6.4 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 PHE A 101 32.81 -98.00 REMARK 500 VAL A 131 -46.61 -134.43 REMARK 500 THR A 181 -52.69 -120.91 REMARK 500 SER A 347 -4.65 107.01 REMARK 500 ALA A 348 78.63 -117.56 REMARK 500 SER A 367 11.83 58.74 REMARK 500 ARG A 401 -125.46 -81.21 REMARK 500 HIS A 402 134.27 167.91 REMARK 500 ASN A 406 64.88 39.71 REMARK 500 ILE A 424 -62.43 -102.38 REMARK 500 CYS A 445 110.28 -165.71 REMARK 500 PRO A 495 153.48 -49.28 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 A2003 DISTANCE = 5.82 ANGSTROMS REMARK 525 HOH A2015 DISTANCE = 7.24 ANGSTROMS REMARK 525 HOH A2047 DISTANCE = 6.74 ANGSTROMS REMARK 525 HOH A2150 DISTANCE = 6.80 ANGSTROMS REMARK 525 HOH A2171 DISTANCE = 6.30 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 MN A1532 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 220 OD2 REMARK 620 2 THR A 221 O 85.2 REMARK 620 3 ASP A 318 OD2 93.9 89.9 REMARK 620 4 HOH A2353 O 106.6 160.1 104.9 REMARK 620 N 1 2 3 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 ASP A 318 OD1 100.3 REMARK 620 3 ASP A 319 OD1 93.2 99.9 REMARK 620 N 1 2 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 POO A1534 REMARK 900 REMARK 900 RELATED ENTRIES 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- DEPENDENT RIBONUCLEIC ACID REMARK 900 POLYMERASE REMARK 900 RELATED ID: 1CSJ RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE RIBONUCLEIC ACID- DEPENDENT RIBONUCLEIC REMARK 900 ACID POLYMERASE OF HEPATITIS C VIRUS REMARK 900 RELATED ID: 1CU1 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF AN ENZYME COMPLEX FROM HEPATITIS C VIRUS REMARK 900 RELATED ID: 1GX5 RELATED DB: PDB REMARK 900 HEPATITIS C VIRUS RNA POLYMERASE IN COMPLEX WITH GTP AND MANGANESE REMARK 900 RELATED ID: 1GX6 RELATED DB: PDB REMARK 900 HEPATITIS C VIRUS RNA POLYMERASE IN COMPLEX WITH UTP AND MANGANESE REMARK 900 RELATED ID: 1JXP RELATED DB: PDB REMARK 900 BK STRAIN HEPATITIS C VIRUS (HCV) NS3-NS4A REMARK 900 RELATED ID: 1NS3 RELATED DB: PDB REMARK 900 STRUCTURE OF HCV PROTEASE (BK STRAIN) REMARK 900 RELATED ID: 1QUV RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE RIBONUCLEIC ACID DIRECTED RIBONUCLEIC ACID REMARK 900 POLYMERASE OF HEPATITIS C VIRUS REMARK 900 RELATED ID: 2BRK RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HEPATITIS C VIRUS POLYMERASE IN COMPLEX WITH REMARK 900 AN ALLOSTERIC INHIBITOR (COMPOUND 1) REMARK 900 RELATED ID: 8OHM RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF RIBONUCLEIC ACID HELICASE FROM GENOTYPE 1B REMARK 900 HEPATITIS C VIRUS: MECHANISM OF UNWINDING DUPLEX RIBONUCLEIC ACID REMARK 999 REMARK 999 SEQUENCE REMARK 999 GENOTYPE 1B, STRAIN BK DBREF 2BRL A 1 536 UNP P26663 POLG_HCVBK 2420 2955 SEQRES 1 A 536 SER MET SER TYR THR TRP THR GLY ALA LEU ILE THR PRO SEQRES 2 A 536 CYS ALA ALA GLU GLU SER LYS LEU PRO ILE ASN ALA LEU SEQRES 3 A 536 SER ASN SER LEU LEU ARG HIS HIS ASN MET VAL TYR ALA SEQRES 4 A 536 THR THR SER ARG SER ALA GLY LEU ARG GLN LYS LYS VAL SEQRES 5 A 536 THR PHE ASP ARG LEU GLN VAL LEU ASP ASP HIS TYR ARG SEQRES 6 A 536 ASP VAL LEU LYS GLU MET LYS ALA LYS ALA SER THR VAL SEQRES 7 A 536 LYS ALA LYS LEU LEU SER VAL GLU GLU ALA CYS LYS LEU SEQRES 8 A 536 THR PRO PRO HIS SER ALA LYS SER LYS PHE GLY TYR GLY SEQRES 9 A 536 ALA LYS ASP VAL ARG ASN LEU SER SER LYS ALA VAL ASN SEQRES 10 A 536 HIS ILE HIS SER VAL TRP LYS ASP LEU LEU GLU ASP THR SEQRES 11 A 536 VAL THR PRO ILE ASP THR THR ILE MET ALA LYS ASN GLU SEQRES 12 A 536 VAL PHE CYS VAL GLN PRO GLU LYS GLY GLY ARG LYS PRO SEQRES 13 A 536 ALA ARG LEU ILE VAL PHE PRO ASP LEU GLY VAL ARG VAL SEQRES 14 A 536 CYS GLU LYS MET ALA LEU TYR ASP VAL VAL SER THR LEU SEQRES 15 A 536 PRO GLN VAL VAL MET GLY SER SER TYR GLY PHE GLN TYR SEQRES 16 A 536 SER PRO GLY GLN ARG VAL GLU PHE LEU VAL ASN THR TRP SEQRES 17 A 536 LYS SER LYS LYS ASN PRO MET GLY PHE SER TYR ASP THR SEQRES 18 A 536 ARG CYS PHE ASP SER THR VAL THR GLU ASN ASP ILE ARG SEQRES 19 A 536 VAL GLU GLU SER ILE TYR GLN CYS CYS ASP LEU ALA PRO SEQRES 20 A 536 GLU ALA ARG GLN ALA ILE LYS SER LEU THR GLU ARG LEU SEQRES 21 A 536 TYR ILE GLY GLY PRO LEU THR ASN SER LYS GLY GLN ASN SEQRES 22 A 536 CYS GLY TYR ARG ARG CYS ARG ALA SER GLY VAL LEU THR SEQRES 23 A 536 THR SER CYS GLY ASN THR LEU THR CYS TYR LEU LYS ALA SEQRES 24 A 536 SER ALA ALA CYS ARG ALA ALA LYS LEU GLN ASP CYS THR SEQRES 25 A 536 MET LEU VAL ASN GLY ASP ASP LEU VAL VAL ILE CYS GLU SEQRES 26 A 536 SER ALA GLY THR GLN GLU ASP ALA ALA SER LEU ARG VAL SEQRES 27 A 536 PHE THR GLU ALA MET THR ARG TYR SER ALA PRO PRO GLY SEQRES 28 A 536 ASP PRO PRO GLN PRO GLU TYR ASP LEU GLU LEU ILE THR SEQRES 29 A 536 SER CYS SER SER ASN VAL SER VAL ALA HIS ASP ALA SER SEQRES 30 A 536 GLY LYS ARG VAL TYR TYR LEU THR ARG ASP PRO THR THR SEQRES 31 A 536 PRO LEU ALA ARG ALA ALA TRP GLU THR ALA ARG HIS THR SEQRES 32 A 536 PRO VAL ASN SER TRP LEU GLY ASN ILE ILE MET TYR ALA SEQRES 33 A 536 PRO THR LEU TRP ALA ARG MET ILE LEU MET THR HIS PHE SEQRES 34 A 536 PHE SER ILE LEU LEU ALA GLN GLU GLN LEU GLU LYS ALA SEQRES 35 A 536 LEU ASP CYS GLN ILE TYR GLY ALA CYS TYR SER ILE GLU SEQRES 36 A 536 PRO LEU ASP LEU PRO GLN ILE ILE GLU ARG LEU HIS GLY SEQRES 37 A 536 LEU SER ALA PHE SER LEU HIS SER TYR SER PRO GLY GLU SEQRES 38 A 536 ILE ASN ARG VAL ALA SER CYS LEU ARG LYS LEU GLY VAL SEQRES 39 A 536 PRO PRO LEU ARG VAL TRP ARG HIS ARG ALA ARG SER VAL SEQRES 40 A 536 ARG ALA ARG LEU LEU SER GLN GLY GLY ARG ALA ALA THR SEQRES 41 A 536 CYS GLY LYS TYR LEU PHE ASN TRP ALA VAL LYS THR LYS SEQRES 42 A 536 LEU LYS LEU HET MN A1532 1 HET MN A1533 1 HET POO A1534 37 HETNAM MN MANGANESE (II) ION HETNAM POO 3-CYCLOHEXYL-1-(2-{METHYL[(1-METHYLPIPERIDIN-3-YL) HETNAM 2 POO METHYL]AMINO}-2-OXOETHYL)-2-PHENYL-1H-INDOLE-6- HETNAM 3 POO CARBOXYLIC ACID FORMUL 2 MN 2(MN 2+) FORMUL 4 POO C31 H39 N3 O3 FORMUL 5 HOH *354(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 SER A 180 1 17 HELIX 8 8 THR A 181 GLY A 188 1 8 HELIX 9 9 GLY A 192 TYR A 195 5 4 HELIX 10 10 SER A 196 SER A 210 1 15 HELIX 11 11 CYS A 223 VAL A 228 1 6 HELIX 12 12 THR A 229 GLN A 241 1 13 HELIX 13 13 ALA A 246 LEU A 260 1 15 HELIX 14 14 THR A 286 ALA A 306 1 21 HELIX 15 15 GLY A 328 TYR A 346 1 19 HELIX 16 16 ASP A 359 ILE A 363 5 5 HELIX 17 17 PRO A 388 ARG A 401 1 14 HELIX 18 18 ASN A 406 TYR A 415 1 10 HELIX 19 19 THR A 418 ILE A 424 1 7 HELIX 20 20 ILE A 424 GLN A 436 1 13 HELIX 21 21 GLU A 455 LEU A 457 5 3 HELIX 22 22 ASP A 458 GLY A 468 1 11 HELIX 23 23 LEU A 469 SER A 473 5 5 HELIX 24 24 SER A 478 GLY A 493 1 16 HELIX 25 25 PRO A 496 GLN A 514 1 19 HELIX 26 26 GLY A 515 PHE A 526 1 12 HELIX 27 27 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 PRO A 163 -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 SER A 368 HIS A 374 0 SHEET 2 AD 2 ARG A 380 ARG A 386 -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 OD2 ASP A 220 MN MN A1532 1555 1555 2.31 LINK OD1 ASP A 220 MN MN A1533 1555 1555 2.39 LINK O THR A 221 MN MN A1532 1555 1555 2.14 LINK OD2 ASP A 318 MN MN A1532 1555 1555 2.29 LINK OD1 ASP A 318 MN MN A1533 1555 1555 2.10 LINK OD1 ASP A 319 MN MN A1533 1555 1555 2.39 LINK MN MN A1532 O HOH A2353 1555 1555 2.59 SITE 1 AC1 7 ASP A 220 THR A 221 ASP A 318 MN A1533 SITE 2 AC1 7 HOH A2352 HOH A2353 HOH A2354 SITE 1 AC2 5 ASP A 220 ASP A 318 ASP A 319 MN A1532 SITE 2 AC2 5 HOH A2353 SITE 1 AC3 9 VAL A 37 LEU A 392 ALA A 393 ALA A 396 SITE 2 AC3 9 ILE A 424 HIS A 428 LEU A 492 PRO A 495 SITE 3 AC3 9 ARG A 503 CRYST1 68.303 94.854 96.230 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 0.014641 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010543 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010392 0.00000