HEADER IMMUNE SYSTEM/RNA 16-JAN-17 5UJ2 TITLE CRYSTAL STRUCTURE OF HCV NS5B GENOTYPE 2A JFH-1 ISOLATE WITH S15G E86Q TITLE 2 E87Q C223H V321I MUTATIONS AND DELTA8 NETA HAIRPOIN LOOP DELETION IN TITLE 3 COMPLEX WITH GS-639476 (DIPHSOHATE VERSION OF GS-9813), MN2+ AND TITLE 4 SYMMETRICAL PRIMER TEMPLATE 5'-AUAAAUUU COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (5'-R(*AP*UP*AP*AP*AP*UP*UP*U)-3'); COMPND 3 CHAIN: T, P; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: GENOME POLYPROTEIN; COMPND 7 CHAIN: A; COMPND 8 ENGINEERED: YES; COMPND 9 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: ROSETTA(DE3); SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: VCID 6258; SOURCE 9 MOL_ID: 2; SOURCE 10 ORGANISM_SCIENTIFIC: HEPATITIS C VIRUS; SOURCE 11 ORGANISM_TAXID: 11103; SOURCE 12 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 13 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS HCV, VIRAL, NS5B, RDRP, RESISTANCE MUTATION, SOFOSBUVIR, SOVALDI, KEYWDS 2 VIRUNON, GS7977-DP, GS-639476, TEMPLATE, PRIMER, IMMUNE SYSTEM-RNA KEYWDS 3 COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR T.E.EDWARDS,D.FOX III,T.C.APPLEBY,E.MURAKAMI,A.REY,M.E.MCGRATH REVDAT 3 04-OCT-23 5UJ2 1 LINK REVDAT 2 12-APR-17 5UJ2 1 JRNL REVDAT 1 22-MAR-17 5UJ2 0 JRNL AUTH T.A.KIRSCHBERG,S.METOBO,M.O.CLARKE,V.AKTOUDIANAKIS, JRNL AUTH 2 D.BABUSIS,O.BARAUSKAS,G.BIRKUS,T.BUTLER,D.BYUN,G.CHIN, JRNL AUTH 3 E.DOERFFLER,T.E.EDWARDS,M.FENAUX,R.LEE,W.LEW,M.R.MISH, JRNL AUTH 4 E.MURAKAMI,Y.PARK,N.H.SQUIRES,N.TIRUNAGARI,T.WANG, JRNL AUTH 5 M.WHITCOMB,J.XU,H.YANG,H.YE,L.ZHANG,T.C.APPLEBY,J.Y.FENG, JRNL AUTH 6 A.S.RAY,A.CHO,C.U.KIM JRNL TITL DISCOVERY OF A 2'-FLUORO-2'-C-METHYL C-NUCLEOTIDE HCV JRNL TITL 2 POLYMERASE INHIBITOR AND A PHOSPHORAMIDATE PRODRUG WITH JRNL TITL 3 FAVORABLE PROPERTIES. JRNL REF BIOORG. MED. CHEM. LETT. V. 27 1840 2017 JRNL REFN ESSN 1464-3405 JRNL PMID 28274633 JRNL DOI 10.1016/J.BMCL.2017.02.037 REMARK 2 REMARK 2 RESOLUTION. 2.90 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) : 2.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 23025 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) : 0.186 REMARK 3 R VALUE (WORKING SET) : 0.184 REMARK 3 FREE R VALUE : 0.227 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1167 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4056 REMARK 3 NUCLEIC ACID ATOMS : 252 REMARK 3 HETEROGEN ATOMS : 32 REMARK 3 SOLVENT ATOMS : 25 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 54.08 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 57.85 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.70000 REMARK 3 B22 (A**2) : 1.70000 REMARK 3 B33 (A**2) : -5.52000 REMARK 3 B12 (A**2) : 0.85000 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): 0.543 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.300 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.256 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 14.568 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : NULL ; NULL REMARK 3 ANGLE DISTANCE (A) : NULL ; NULL REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : NULL ; NULL REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : NULL ; NULL REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : NULL ; NULL REMARK 3 MULTIPLE TORSION (A) : NULL ; NULL REMARK 3 H-BOND (X...Y) (A) : NULL ; NULL 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) : NULL ; NULL REMARK 3 STAGGERED (DEGREES) : NULL ; NULL REMARK 3 TRANSVERSE (DEGREES) : NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 4 REMARK 4 5UJ2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-JAN-17. REMARK 100 THE DEPOSITION ID IS D_1000225950. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-DEC-13 REMARK 200 TEMPERATURE (KELVIN) : 100.000 REMARK 200 PH : 6.60 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 21-ID-G REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97872 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX-300 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23027 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.900 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : 0.08500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.7700 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER, PHASER REMARK 200 STARTING MODEL: 4WT9 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 70.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.10 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NS5B AT 5.1 MG/ML IN 5 MM TRIS PH 7.5, REMARK 280 200 MM NH4OAC, 1 MM EDTA, 1 MM DTT AGAINST 25% PEG 550, PH 6.60, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/6 REMARK 290 6555 X-Y,X,Z+5/6 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 60.74000 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 30.37000 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 45.55500 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 15.18500 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 75.92500 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4230 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 22420 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -56.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: T, P, 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 A P 1 REMARK 465 U P 2 REMARK 465 MET A -1 REMARK 465 ALA A 542 REMARK 465 ARG A 543 REMARK 465 LEU A 544 REMARK 465 LEU A 545 REMARK 465 ASP A 546 REMARK 465 LEU A 547 REMARK 465 SER A 548 REMARK 465 SER A 549 REMARK 465 TRP A 550 REMARK 465 PHE A 551 REMARK 465 THR A 552 REMARK 465 VAL A 553 REMARK 465 GLY A 554 REMARK 465 ALA A 555 REMARK 465 GLY A 556 REMARK 465 GLY A 557 REMARK 465 GLY A 558 REMARK 465 ASP A 559 REMARK 465 ILE A 560 REMARK 465 PHE A 561 REMARK 465 HIS A 562 REMARK 465 SER A 563 REMARK 465 VAL A 564 REMARK 465 SER A 565 REMARK 465 ARG A 566 REMARK 465 ALA A 567 REMARK 465 ARG A 568 REMARK 465 PRO A 569 REMARK 465 ARG A 570 REMARK 465 LEU A 571 REMARK 465 GLU A 572 REMARK 465 HIS A 573 REMARK 465 HIS A 574 REMARK 465 HIS A 575 REMARK 465 HIS A 576 REMARK 465 HIS A 577 REMARK 465 HIS A 578 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 A T 1 O5' C5' C4' O4' C3' C2' O2' REMARK 470 A T 1 C1' N9 C8 N7 C5 C6 N6 REMARK 470 A T 1 N1 C2 N3 C4 REMARK 470 A P 3 P OP1 OP2 O5' C5' C4' O4' REMARK 470 A P 3 C3' C2' O2' C1' N9 C8 N7 REMARK 470 A P 3 C5 C6 N6 N1 C2 N3 C4 REMARK 470 CYS A 14 SG REMARK 470 GLU A 18 CG CD OE1 OE2 REMARK 470 LYS A 43 CG CD CE NZ REMARK 470 LYS A 50 CG CD CE NZ REMARK 470 LYS A 51 CG CD CE NZ REMARK 470 LYS A 69 CG CD CE NZ REMARK 470 LEU A 73 CG CD1 CD2 REMARK 470 LYS A 106 CG CD CE NZ REMARK 470 LYS A 151 CG CD CE NZ REMARK 470 GLU A 202 CG CD OE1 OE2 REMARK 470 LYS A 206 CG CD CE NZ REMARK 470 LYS A 212 CG CD CE NZ REMARK 470 LYS A 270 CG CD CE NZ REMARK 470 GLU A 330 CG CD OE1 OE2 REMARK 470 ARG A 377 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 379 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 381 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 401 CG CD NE CZ NH1 NH2 REMARK 470 ASP A 440 CG OD1 OD2 REMARK 470 GLN A 441 CG CD OE1 NE2 REMARK 470 TYR A 444 CB CG CD1 CD2 CE1 CE2 CZ REMARK 470 TYR A 444 OH REMARK 470 ARG A 465 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 501 CG CD CE NZ REMARK 470 LYS A 531 CG CD CE NZ REMARK 470 THR A 532 OG1 CG2 REMARK 470 LYS A 533 CG CD CE NZ REMARK 470 LYS A 535 CG CD CE NZ REMARK 470 GLU A 541 CG CD OE1 OE2 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 ALA A 62 -38.61 -38.84 REMARK 500 TYR A 101 40.34 -86.45 REMARK 500 GLN A 131 -48.90 -148.36 REMARK 500 ASP A 213 80.06 -152.73 REMARK 500 ALA A 348 73.33 -152.49 REMARK 500 VAL A 424 -70.62 -97.76 REMARK 500 PRO A 456 -37.00 -38.79 REMARK 500 THR A 476 64.82 63.94 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 P 601 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 U P 8 O3' REMARK 620 2 8B4 P 602 O2A 101.8 REMARK 620 3 HOH P 702 O 84.6 90.3 REMARK 620 4 ASP A 220 OD1 149.4 94.5 121.3 REMARK 620 5 ASP A 318 OD1 68.6 93.8 153.2 84.7 REMARK 620 6 ASP A 319 OD1 65.4 162.7 99.6 92.4 71.1 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 601 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 8B4 P 602 O3B REMARK 620 2 8B4 P 602 O2A 82.6 REMARK 620 3 HOH P 701 O 70.4 88.7 REMARK 620 4 ASP A 220 OD2 145.8 99.1 75.5 REMARK 620 5 THR A 221 O 88.5 166.6 78.9 82.7 REMARK 620 6 ASP A 318 OD2 106.2 100.6 169.8 107.1 91.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 602 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 237 OE2 REMARK 620 2 HIS A 254 ND1 84.5 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN P 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 8B4 P 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN A 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN A 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 603 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4WTG RELATED DB: PDB REMARK 900 HCV POLYMERASE TERNARY STRUCTURE WITH DIPHOSPHATE VERSION OF REMARK 900 SOFOSBUVIR REMARK 900 RELATED ID: 4WTD RELATED DB: PDB REMARK 900 HCV POLYMERASE TERNARY STRUCTURE WITH ADP DBREF 5UJ2 T 1 8 PDB 5UJ2 5UJ2 1 8 DBREF 5UJ2 P 1 8 PDB 5UJ2 5UJ2 1 8 DBREF 5UJ2 A 1 570 UNP R9TEU1 R9TEU1_9HEPC 2443 3012 SEQADV 5UJ2 MET A -1 UNP R9TEU1 INITIATING METHIONINE SEQADV 5UJ2 SER A 0 UNP R9TEU1 EXPRESSION TAG SEQADV 5UJ2 GLY A 15 UNP R9TEU1 SER 2457 ENGINEERED MUTATION SEQADV 5UJ2 GLN A 86 UNP R9TEU1 GLU 2528 ENGINEERED MUTATION SEQADV 5UJ2 GLN A 87 UNP R9TEU1 GLU 2529 ENGINEERED MUTATION SEQADV 5UJ2 HIS A 223 UNP R9TEU1 CYS 2665 ENGINEERED MUTATION SEQADV 5UJ2 ILE A 321 UNP R9TEU1 VAL 2763 ENGINEERED MUTATION SEQADV 5UJ2 A UNP R9TEU1 ASN 2886 DELETION SEQADV 5UJ2 A UNP R9TEU1 PHE 2887 DELETION SEQADV 5UJ2 A UNP R9TEU1 GLU 2888 DELETION SEQADV 5UJ2 A UNP R9TEU1 MET 2889 DELETION SEQADV 5UJ2 A UNP R9TEU1 TYR 2890 DELETION SEQADV 5UJ2 A UNP R9TEU1 GLY 2891 DELETION SEQADV 5UJ2 A UNP R9TEU1 SER 2892 DELETION SEQADV 5UJ2 A UNP R9TEU1 VAL 2893 DELETION SEQADV 5UJ2 GLY A 445 UNP R9TEU1 SER 2895 CONFLICT SEQADV 5UJ2 LEU A 571 UNP R9TEU1 EXPRESSION TAG SEQADV 5UJ2 GLU A 572 UNP R9TEU1 EXPRESSION TAG SEQADV 5UJ2 HIS A 573 UNP R9TEU1 EXPRESSION TAG SEQADV 5UJ2 HIS A 574 UNP R9TEU1 EXPRESSION TAG SEQADV 5UJ2 HIS A 575 UNP R9TEU1 EXPRESSION TAG SEQADV 5UJ2 HIS A 576 UNP R9TEU1 EXPRESSION TAG SEQADV 5UJ2 HIS A 577 UNP R9TEU1 EXPRESSION TAG SEQADV 5UJ2 HIS A 578 UNP R9TEU1 EXPRESSION TAG SEQRES 1 T 8 A U A A A U U U SEQRES 1 P 8 A U A A A U U U SEQRES 1 A 572 MET SER SER MET SER TYR SER TRP THR GLY ALA LEU ILE SEQRES 2 A 572 THR PRO CYS GLY PRO GLU GLU GLU LYS LEU PRO ILE ASN SEQRES 3 A 572 PRO LEU SER ASN SER LEU LEU ARG TYR HIS ASN LYS VAL SEQRES 4 A 572 TYR CYS THR THR SER LYS SER ALA SER GLN ARG ALA LYS SEQRES 5 A 572 LYS VAL THR PHE ASP ARG THR GLN VAL LEU ASP ALA HIS SEQRES 6 A 572 TYR ASP SER VAL LEU LYS ASP ILE LYS LEU ALA ALA SER SEQRES 7 A 572 LYS VAL SER ALA ARG LEU LEU THR LEU GLN GLN ALA CYS SEQRES 8 A 572 GLN LEU THR PRO PRO HIS SER ALA ARG SER LYS TYR GLY SEQRES 9 A 572 PHE GLY ALA LYS GLU VAL ARG SER LEU SER GLY ARG ALA SEQRES 10 A 572 VAL ASN HIS ILE LYS SER VAL TRP LYS ASP LEU LEU GLU SEQRES 11 A 572 ASP PRO GLN THR PRO ILE PRO THR THR ILE MET ALA LYS SEQRES 12 A 572 ASN GLU VAL PHE CYS VAL ASP PRO ALA LYS GLY GLY LYS SEQRES 13 A 572 LYS PRO ALA ARG LEU ILE VAL TYR PRO ASP LEU GLY VAL SEQRES 14 A 572 ARG VAL CYS GLU LYS MET ALA LEU TYR ASP ILE THR GLN SEQRES 15 A 572 LYS LEU PRO GLN ALA VAL MET GLY ALA SER TYR GLY PHE SEQRES 16 A 572 GLN TYR SER PRO ALA GLN ARG VAL GLU TYR LEU LEU LYS SEQRES 17 A 572 ALA TRP ALA GLU LYS LYS ASP PRO MET GLY PHE SER TYR SEQRES 18 A 572 ASP THR ARG HIS PHE ASP SER THR VAL THR GLU ARG ASP SEQRES 19 A 572 ILE ARG THR GLU GLU SER ILE TYR GLN ALA CYS SER LEU SEQRES 20 A 572 PRO GLU GLU ALA ARG THR ALA ILE HIS SER LEU THR GLU SEQRES 21 A 572 ARG LEU TYR VAL GLY GLY PRO MET PHE ASN SER LYS GLY SEQRES 22 A 572 GLN THR CYS GLY TYR ARG ARG CYS ARG ALA SER GLY VAL SEQRES 23 A 572 LEU THR THR SER MET GLY ASN THR ILE THR CYS TYR VAL SEQRES 24 A 572 LYS ALA LEU ALA ALA CYS LYS ALA ALA GLY ILE VAL ALA SEQRES 25 A 572 PRO THR MET LEU VAL CYS GLY ASP ASP LEU ILE VAL ILE SEQRES 26 A 572 SER GLU SER GLN GLY THR GLU GLU ASP GLU ARG ASN LEU SEQRES 27 A 572 ARG ALA PHE THR GLU ALA MET THR ARG TYR SER ALA PRO SEQRES 28 A 572 PRO GLY ASP PRO PRO ARG PRO GLU TYR ASP LEU GLU LEU SEQRES 29 A 572 ILE THR SER CYS SER SER ASN VAL SER VAL ALA LEU GLY SEQRES 30 A 572 PRO ARG GLY ARG ARG ARG TYR TYR LEU THR ARG ASP PRO SEQRES 31 A 572 THR THR PRO LEU ALA ARG ALA ALA TRP GLU THR VAL ARG SEQRES 32 A 572 HIS SER PRO ILE ASN SER TRP LEU GLY ASN ILE ILE GLN SEQRES 33 A 572 TYR ALA PRO THR ILE TRP VAL ARG MET VAL LEU MET THR SEQRES 34 A 572 HIS PHE PHE SER ILE LEU MET VAL GLN ASP THR LEU ASP SEQRES 35 A 572 GLN ASN LEU TYR GLY VAL ASN PRO LEU ASP LEU PRO ALA SEQRES 36 A 572 ILE ILE GLU ARG LEU HIS GLY LEU ASP ALA PHE SER MET SEQRES 37 A 572 HIS THR TYR SER HIS HIS GLU LEU THR ARG VAL ALA SER SEQRES 38 A 572 ALA LEU ARG LYS LEU GLY ALA PRO PRO LEU ARG VAL TRP SEQRES 39 A 572 LYS SER ARG ALA ARG ALA VAL ARG ALA SER LEU ILE SER SEQRES 40 A 572 ARG GLY GLY LYS ALA ALA VAL CYS GLY ARG TYR LEU PHE SEQRES 41 A 572 ASN TRP ALA VAL LYS THR LYS LEU LYS LEU THR PRO LEU SEQRES 42 A 572 PRO GLU ALA ARG LEU LEU ASP LEU SER SER TRP PHE THR SEQRES 43 A 572 VAL GLY ALA GLY GLY GLY ASP ILE PHE HIS SER VAL SER SEQRES 44 A 572 ARG ALA ARG PRO ARG LEU GLU HIS HIS HIS HIS HIS HIS HET MN P 601 1 HET 8B4 P 602 28 HET MN A 601 1 HET MN A 602 1 HET CL A 603 1 HETNAM MN MANGANESE (II) ION HETNAM 8B4 (1S)-1-(4-AMINOIMIDAZO[2,1-F][1,2,4]TRIAZIN-7-YL)-1,4- HETNAM 2 8B4 ANHYDRO-2-DEOXY-2-FLUORO-5-O-[(S)- HETNAM 3 8B4 HYDROXY(PHOSPHONOOXY)PHOSPHORYL]-2-METHYL-D-RIBITOL HETNAM CL CHLORIDE ION FORMUL 4 MN 3(MN 2+) FORMUL 5 8B4 C11 H16 F N5 O9 P2 FORMUL 8 CL CL 1- FORMUL 9 HOH *25(H2 O) HELIX 1 AA1 TYR A 33 ASN A 35 5 3 HELIX 2 AA2 THR A 41 LYS A 43 5 3 HELIX 3 AA3 SER A 44 THR A 53 1 10 HELIX 4 AA4 ASP A 61 SER A 76 1 16 HELIX 5 AA5 THR A 84 LEU A 91 1 8 HELIX 6 AA6 GLY A 104 LEU A 111 1 8 HELIX 7 AA7 SER A 112 ASP A 129 1 18 HELIX 8 AA8 ASP A 148 GLY A 152 5 5 HELIX 9 AA9 ASP A 164 GLY A 188 1 25 HELIX 10 AB1 ALA A 189 TYR A 195 5 7 HELIX 11 AB2 SER A 196 LYS A 211 1 16 HELIX 12 AB3 HIS A 223 VAL A 228 1 6 HELIX 13 AB4 THR A 229 ALA A 242 1 14 HELIX 14 AB5 PRO A 246 LEU A 260 1 15 HELIX 15 AB6 LEU A 285 GLY A 307 1 23 HELIX 16 AB7 GLN A 327 TYR A 346 1 20 HELIX 17 AB8 ASP A 359 ILE A 363 5 5 HELIX 18 AB9 PRO A 388 ALA A 396 1 9 HELIX 19 AC1 PRO A 404 TYR A 415 1 12 HELIX 20 AC2 THR A 418 VAL A 424 1 7 HELIX 21 AC3 VAL A 424 ASP A 437 1 14 HELIX 22 AC4 ASN A 455 LEU A 457 5 3 HELIX 23 AC5 ASP A 458 GLY A 468 1 11 HELIX 24 AC6 LEU A 469 SER A 473 5 5 HELIX 25 AC7 SER A 478 GLY A 493 1 16 HELIX 26 AC8 PRO A 496 ARG A 514 1 19 HELIX 27 AC9 GLY A 515 LEU A 525 1 11 HELIX 28 AD1 PHE A 526 VAL A 530 5 5 SHEET 1 AA1 5 TYR A 4 TRP A 6 0 SHEET 2 AA1 5 THR A 273 ARG A 277 -1 O TYR A 276 N SER A 5 SHEET 3 AA1 5 GLY A 264 PHE A 267 -1 N MET A 266 O CYS A 274 SHEET 4 AA1 5 THR A 136 ALA A 140 1 N ILE A 138 O PHE A 267 SHEET 5 AA1 5 LEU A 159 TYR A 162 -1 O ILE A 160 N MET A 139 SHEET 1 AA2 2 VAL A 37 CYS A 39 0 SHEET 2 AA2 2 VAL A 144 CYS A 146 -1 O PHE A 145 N TYR A 38 SHEET 1 AA3 3 PRO A 214 TYR A 219 0 SHEET 2 AA3 3 ASP A 319 GLU A 325 -1 O SER A 324 N MET A 215 SHEET 3 AA3 3 VAL A 309 CYS A 316 -1 N CYS A 316 O ASP A 319 SHEET 1 AA4 2 ASN A 369 LEU A 374 0 SHEET 2 AA4 2 ARG A 380 THR A 385 -1 O ARG A 381 N ALA A 373 LINK O3' U P 8 MN MN P 601 1555 1555 2.34 LINK MN MN P 601 O2A 8B4 P 602 1555 1555 2.23 LINK MN MN P 601 O HOH P 702 1555 1555 1.97 LINK MN MN P 601 OD1 ASP A 220 1555 1555 2.11 LINK MN MN P 601 OD1 ASP A 318 1555 1555 2.35 LINK MN MN P 601 OD1 ASP A 319 1555 1555 2.03 LINK O3B 8B4 P 602 MN MN A 601 1555 1555 2.12 LINK O2A 8B4 P 602 MN MN A 601 1555 1555 1.96 LINK O HOH P 701 MN MN A 601 1555 1555 2.24 LINK OD2 ASP A 220 MN MN A 601 1555 1555 2.39 LINK O THR A 221 MN MN A 601 1555 1555 2.15 LINK OE2 GLU A 237 MN MN A 602 1555 1555 2.22 LINK ND1 HIS A 254 MN MN A 602 1555 1555 2.48 LINK OD2 ASP A 318 MN MN A 601 1555 1555 2.07 SITE 1 AC1 7 ASP A 220 ASP A 318 ASP A 319 MN A 601 SITE 2 AC1 7 U P 8 8B4 P 602 HOH P 702 SITE 1 AC2 16 ARG A 158 ASP A 220 THR A 221 HIS A 223 SITE 2 AC2 16 PHE A 224 ASP A 225 SER A 282 ASN A 291 SITE 3 AC2 16 ASP A 318 MN A 601 U P 8 MN P 601 SITE 4 AC2 16 HOH P 701 HOH P 702 U T 2 A T 3 SITE 1 AC3 6 ASP A 220 THR A 221 ASP A 318 MN P 601 SITE 2 AC3 6 8B4 P 602 HOH P 701 SITE 1 AC4 2 GLU A 237 HIS A 254 SITE 1 AC5 5 GLY A 375 PRO A 376 ARG A 377 GLY A 378 SITE 2 AC5 5 ARG A 379 CRYST1 141.760 141.760 91.110 90.00 90.00 120.00 P 65 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 0.007054 0.004073 0.000000 0.00000 SCALE2 0.000000 0.008145 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010976 0.00000