HEADER TRANSFERASE 18-SEP-14 4V0Q TITLE DENGUE VIRUS FULL LENGTH NS5 COMPLEXED WITH SAH COMPND MOL_ID: 1; COMPND 2 MOLECULE: NS5 POLYMERASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 2494-3385; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DENGUE VIRUS 3; SOURCE 3 ORGANISM_TAXID: 11069; SOURCE 4 STRAIN: SINGAPORE STRAIN; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 8 EXPRESSION_SYSTEM_VARIANT: CODON PLUS; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_VECTOR: PNIC28-BSA4 KEYWDS TRANSFERASE, METHYLTRANSFERASE, RNA-DEPENDENT RNA POLYMERASE EXPDTA X-RAY DIFFRACTION AUTHOR Y.ZHAO,S.SOH,J.ZHENG,W.W.PHOO,K.SWAMINATHAN,T.C.CORNVIK,S.P.LIM,P.- AUTHOR 2 Y.SHI,J.LESCAR,S.G.VASUDEVAN,D.LUO REVDAT 4 10-JAN-24 4V0Q 1 REMARK LINK REVDAT 3 20-JUN-18 4V0Q 1 TITLE REMARK REVDAT 2 25-MAR-15 4V0Q 1 JRNL REVDAT 1 28-JAN-15 4V0Q 0 JRNL AUTH Y.ZHAO,T.S.SOH,J.ZHENG,K.W.K.CHAN,W.W.PHOO,C.C.LEE, JRNL AUTH 2 M.Y.F.TAY,K.SWAMINATHAN,T.C.CORNVIK,S.P.LIM,P.SHI,J.LESCAR, JRNL AUTH 3 S.G.VASUDEVAN,D.LUO JRNL TITL A CRYSTAL STRUCTURE OF THE DENGUE VIRUS NS5 PROTEIN REVEALS JRNL TITL 2 A NOVEL INTER-DOMAIN INTERFACE ESSENTIAL FOR PROTEIN JRNL TITL 3 FLEXIBILITY AND VIRUS REPLICATION. JRNL REF PLOS PATHOG. V. 11 04682 2015 JRNL REFN ISSN 1553-7366 JRNL PMID 25775415 JRNL DOI 10.1371/JOURNAL.PPAT.1004682 REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.18 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 91.2 REMARK 3 NUMBER OF REFLECTIONS : 41182 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.194 REMARK 3 R VALUE (WORKING SET) : 0.191 REMARK 3 FREE R VALUE : 0.246 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2075 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 39.1898 - 5.6670 0.88 2673 168 0.1762 0.2209 REMARK 3 2 5.6670 - 4.5001 0.92 2670 145 0.1611 0.2234 REMARK 3 3 4.5001 - 3.9319 0.93 2694 139 0.1485 0.1680 REMARK 3 4 3.9319 - 3.5727 0.92 2645 136 0.1687 0.2191 REMARK 3 5 3.5727 - 3.3167 0.89 2553 120 0.1781 0.2620 REMARK 3 6 3.3167 - 3.1213 0.93 2685 129 0.1974 0.2850 REMARK 3 7 3.1213 - 2.9650 0.94 2668 133 0.2055 0.2880 REMARK 3 8 2.9650 - 2.8360 0.94 2687 150 0.2194 0.2651 REMARK 3 9 2.8360 - 2.7268 0.94 2652 140 0.2129 0.2482 REMARK 3 10 2.7268 - 2.6328 0.94 2660 149 0.2209 0.3143 REMARK 3 11 2.6328 - 2.5505 0.94 2626 153 0.2283 0.2507 REMARK 3 12 2.5505 - 2.4776 0.92 2614 131 0.2371 0.3481 REMARK 3 13 2.4776 - 2.4124 0.86 2432 122 0.2340 0.3174 REMARK 3 14 2.4124 - 2.3535 0.87 2433 121 0.2545 0.2875 REMARK 3 15 2.3535 - 2.3000 0.87 2415 139 0.2730 0.3520 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.260 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.860 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.004 7047 REMARK 3 ANGLE : 0.803 9533 REMARK 3 CHIRALITY : 0.033 1021 REMARK 3 PLANARITY : 0.003 1223 REMARK 3 DIHEDRAL : 14.063 2643 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 5 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 6 THROUGH 263 ) REMARK 3 ORIGIN FOR THE GROUP (A): 19.1812 134.9892 18.4777 REMARK 3 T TENSOR REMARK 3 T11: 0.1417 T22: 0.1354 REMARK 3 T33: 0.1114 T12: -0.0229 REMARK 3 T13: -0.0229 T23: -0.0034 REMARK 3 L TENSOR REMARK 3 L11: 0.7595 L22: 0.8858 REMARK 3 L33: 0.3901 L12: -0.1164 REMARK 3 L13: 0.0590 L23: 0.1721 REMARK 3 S TENSOR REMARK 3 S11: -0.0046 S12: 0.0333 S13: -0.0225 REMARK 3 S21: -0.0837 S22: 0.0431 S23: 0.0708 REMARK 3 S31: -0.0179 S32: 0.0274 S33: 0.0001 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 264 THROUGH 321 ) REMARK 3 ORIGIN FOR THE GROUP (A): 10.8371 157.5592 38.7397 REMARK 3 T TENSOR REMARK 3 T11: 0.1536 T22: 0.1808 REMARK 3 T33: 0.2987 T12: -0.0334 REMARK 3 T13: 0.0387 T23: -0.0173 REMARK 3 L TENSOR REMARK 3 L11: 0.4410 L22: 0.4173 REMARK 3 L33: 0.2820 L12: -0.0120 REMARK 3 L13: -0.2140 L23: 0.2715 REMARK 3 S TENSOR REMARK 3 S11: -0.0154 S12: -0.0146 S13: -0.0366 REMARK 3 S21: 0.1826 S22: 0.0411 S23: 0.1925 REMARK 3 S31: 0.1308 S32: -0.0596 S33: -0.0242 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 322 THROUGH 403 ) REMARK 3 ORIGIN FOR THE GROUP (A): 26.2510 170.8483 30.2458 REMARK 3 T TENSOR REMARK 3 T11: 0.2008 T22: 0.2355 REMARK 3 T33: 0.1810 T12: -0.0265 REMARK 3 T13: -0.0266 T23: -0.0099 REMARK 3 L TENSOR REMARK 3 L11: 0.4008 L22: 0.2934 REMARK 3 L33: -0.0056 L12: 0.2593 REMARK 3 L13: 0.0027 L23: -0.0938 REMARK 3 S TENSOR REMARK 3 S11: -0.1046 S12: 0.1078 S13: 0.0187 REMARK 3 S21: 0.0068 S22: 0.0740 S23: 0.1119 REMARK 3 S31: 0.0222 S32: -0.0615 S33: 0.0123 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 404 THROUGH 722 ) REMARK 3 ORIGIN FOR THE GROUP (A): 31.5467 173.4461 35.7732 REMARK 3 T TENSOR REMARK 3 T11: 0.1812 T22: 0.1709 REMARK 3 T33: 0.1762 T12: 0.0004 REMARK 3 T13: -0.0128 T23: -0.0122 REMARK 3 L TENSOR REMARK 3 L11: 0.5731 L22: 0.4401 REMARK 3 L33: 0.2839 L12: 0.1255 REMARK 3 L13: 0.0037 L23: 0.0996 REMARK 3 S TENSOR REMARK 3 S11: -0.0532 S12: 0.0111 S13: 0.0151 REMARK 3 S21: -0.0055 S22: -0.0510 S23: 0.0200 REMARK 3 S31: 0.0182 S32: -0.0062 S33: -0.0036 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 723 THROUGH 883 ) REMARK 3 ORIGIN FOR THE GROUP (A): 26.4123 182.6688 5.7367 REMARK 3 T TENSOR REMARK 3 T11: 0.4062 T22: 0.5129 REMARK 3 T33: 0.3788 T12: 0.0293 REMARK 3 T13: -0.0159 T23: -0.0255 REMARK 3 L TENSOR REMARK 3 L11: 0.2760 L22: 0.1915 REMARK 3 L33: 0.5920 L12: -0.1340 REMARK 3 L13: 0.3460 L23: -0.0560 REMARK 3 S TENSOR REMARK 3 S11: -0.0607 S12: 0.0296 S13: -0.0114 REMARK 3 S21: 0.0398 S22: -0.0861 S23: 0.0535 REMARK 3 S31: -0.1302 S32: -0.3668 S33: -0.0002 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4V0Q COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 18-SEP-14. REMARK 100 THE DEPOSITION ID IS D_1290061785. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-FEB-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X10SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 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 : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 41247 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 39.180 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.600 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 91.8 REMARK 200 DATA REDUNDANCY : 3.500 REMARK 200 R MERGE (I) : 0.08000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.5000 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: NULL REMARK 200 STARTING MODEL: PDB ENTRIES 3P97 AND 2J7U REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.20 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.42 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 47.56450 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 75.72250 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 47.56450 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 75.72250 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5300 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 70920 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -17.1 KCAL/MOL 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 95.12900 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 302.89000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A2134 LIES ON A SPECIAL POSITION. REMARK 375 HOH A2135 LIES ON A SPECIAL POSITION. REMARK 375 HOH A2142 LIES ON A SPECIAL POSITION. 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 SER A 4 REMARK 465 MET A 5 REMARK 465 ALA A 406 REMARK 465 ALA A 407 REMARK 465 MET A 408 REMARK 465 GLY A 409 REMARK 465 ALA A 410 REMARK 465 VAL A 411 REMARK 465 PHE A 412 REMARK 465 THR A 413 REMARK 465 GLU A 414 REMARK 465 GLU A 415 REMARK 465 ASN A 416 REMARK 465 GLN A 417 REMARK 465 GLY A 455 REMARK 465 LYS A 456 REMARK 465 ARG A 457 REMARK 465 GLU A 458 REMARK 465 LYS A 459 REMARK 465 LYS A 460 REMARK 465 LEU A 461 REMARK 465 GLY A 462 REMARK 465 GLU A 463 REMARK 465 PHE A 464 REMARK 465 GLY A 465 REMARK 465 LYS A 466 REMARK 465 ALA A 467 REMARK 465 LYS A 468 REMARK 465 GLY A 469 REMARK 465 PRO A 884 REMARK 465 SER A 885 REMARK 465 MET A 886 REMARK 465 LYS A 887 REMARK 465 ARG A 888 REMARK 465 PHE A 889 REMARK 465 ARG A 890 REMARK 465 LYS A 891 REMARK 465 GLU A 892 REMARK 465 GLU A 893 REMARK 465 GLU A 894 REMARK 465 SER A 895 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 MET A 342 CG SD CE REMARK 470 TRP A 418 CG CD1 CD2 NE1 CE2 CE3 CZ2 REMARK 470 TRP A 418 CZ3 CH2 REMARK 470 MET A 454 CG SD CE REMARK 470 ARG A 471 CG CD NE CZ NH1 NH2 REMARK 470 GLN A 742 CG CD OE1 NE2 REMARK 470 TRP A 746 CG CD1 CD2 NE1 CE2 CE3 CZ2 REMARK 470 TRP A 746 CZ3 CH2 REMARK 470 SER A 791 OG REMARK 470 ARG A 792 CG CD NE CZ NH1 NH2 REMARK 470 TRP A 795 CG CD1 CD2 NE1 CE2 CE3 CZ2 REMARK 470 TRP A 795 CZ3 CH2 REMARK 470 ARG A 842 CG CD NE CZ NH1 NH2 REMARK 470 TRP A 846 CG CD1 CD2 NE1 CE2 CE3 CZ2 REMARK 470 TRP A 846 CZ3 CH2 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 O PRO A 367 O HOH A 2156 1.96 REMARK 500 O HOH A 2029 O HOH A 2086 1.99 REMARK 500 O HOH A 2104 O HOH A 2105 2.01 REMARK 500 ND2 ASN A 492 O HOH A 2196 2.05 REMARK 500 O HOH A 2014 O HOH A 2018 2.10 REMARK 500 O HOH A 2049 O HOH A 2067 2.10 REMARK 500 OE1 GLU A 428 O HOH A 2183 2.10 REMARK 500 OE1 GLU A 74 O HOH A 2038 2.14 REMARK 500 O HOH A 2040 O HOH A 2099 2.15 REMARK 500 OG1 THR A 104 O HOH A 2061 2.15 REMARK 500 O ALA A 738 O HOH A 2143 2.16 REMARK 500 OD2 ASP A 294 NH2 ARG A 581 2.18 REMARK 500 O HOH A 2165 O HOH A 2229 2.19 REMARK 500 N HIS A 800 O HOH A 2268 2.19 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 HIS A 52 -46.07 72.13 REMARK 500 LYS A 173 118.23 -163.95 REMARK 500 GLN A 339 35.97 -80.02 REMARK 500 SER A 448 27.78 -142.54 REMARK 500 TYR A 503 -48.44 65.79 REMARK 500 ASN A 574 78.76 -151.96 REMARK 500 ASP A 596 -158.48 -92.86 REMARK 500 GLN A 597 165.52 67.18 REMARK 500 ALA A 744 47.53 -78.06 REMARK 500 LEU A 748 -64.34 53.74 REMARK 500 SER A 791 -166.19 58.37 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1001 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 437 OE2 REMARK 620 2 HIS A 441 NE2 109.7 REMARK 620 3 CYS A 446 SG 99.9 116.5 REMARK 620 4 CYS A 449 SG 119.6 109.6 101.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1002 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 712 NE2 REMARK 620 2 CYS A 728 SG 110.5 REMARK 620 3 CYS A 847 SG 101.8 117.1 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 ZN A 1001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 1002 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SAH A 1051 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 1884 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 1885 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 1886 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 1887 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 1888 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 1889 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1890 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4V0R RELATED DB: PDB REMARK 900 DENGUE VIRUS FULL LENGTH NS5 COMPLEXED WITH GTP AND SAH DBREF 4V0Q A 4 895 UNP Q6DLV0 Q6DLV0_9FLAV 2494 3385 SEQADV 4V0Q MET A 5 UNP Q6DLV0 GLN 2495 CONFLICT SEQADV 4V0Q ILE A 72 UNP Q6DLV0 VAL 2562 CONFLICT SEQADV 4V0Q GLU A 374 UNP Q6DLV0 GLY 2864 CONFLICT SEQRES 1 A 892 SER MET GLY GLU THR LEU GLY GLU LYS TRP LYS LYS LYS SEQRES 2 A 892 LEU ASN GLN LEU SER ARG LYS GLU PHE ASP LEU TYR LYS SEQRES 3 A 892 LYS SER GLY ILE THR GLU VAL ASP ARG THR GLU ALA LYS SEQRES 4 A 892 GLU GLY LEU LYS ARG GLY GLU THR THR HIS HIS ALA VAL SEQRES 5 A 892 SER ARG GLY SER ALA LYS LEU GLN TRP PHE VAL GLU ARG SEQRES 6 A 892 ASN MET VAL ILE PRO GLU GLY ARG VAL ILE ASP LEU GLY SEQRES 7 A 892 CYS GLY ARG GLY GLY TRP SER TYR TYR CYS ALA GLY LEU SEQRES 8 A 892 LYS LYS VAL THR GLU VAL ARG GLY TYR THR LYS GLY GLY SEQRES 9 A 892 PRO GLY HIS GLU GLU PRO VAL PRO MET SER THR TYR GLY SEQRES 10 A 892 TRP ASN ILE VAL LYS LEU MET SER GLY LYS ASP VAL PHE SEQRES 11 A 892 TYR LEU PRO PRO GLU LYS CYS ASP THR LEU LEU CYS ASP SEQRES 12 A 892 ILE GLY GLU SER SER PRO SER PRO THR VAL GLU GLU SER SEQRES 13 A 892 ARG THR ILE ARG VAL LEU LYS MET VAL GLU PRO TRP LEU SEQRES 14 A 892 LYS ASN ASN GLN PHE CYS ILE LYS VAL LEU ASN PRO TYR SEQRES 15 A 892 MET PRO THR VAL ILE GLU HIS LEU GLU ARG LEU GLN ARG SEQRES 16 A 892 LYS HIS GLY GLY MET LEU VAL ARG ASN PRO LEU SER ARG SEQRES 17 A 892 ASN SER THR HIS GLU MET TYR TRP ILE SER ASN GLY THR SEQRES 18 A 892 GLY ASN ILE VAL SER SER VAL ASN MET VAL SER ARG LEU SEQRES 19 A 892 LEU LEU ASN ARG PHE THR MET THR HIS ARG ARG PRO THR SEQRES 20 A 892 ILE GLU LYS ASP VAL ASP LEU GLY ALA GLY THR ARG HIS SEQRES 21 A 892 VAL ASN ALA GLU PRO GLU THR PRO ASN MET ASP VAL ILE SEQRES 22 A 892 GLY GLU ARG ILE LYS ARG ILE LYS GLU GLU HIS ASN SER SEQRES 23 A 892 THR TRP HIS TYR ASP ASP GLU ASN PRO TYR LYS THR TRP SEQRES 24 A 892 ALA TYR HIS GLY SER TYR GLU VAL LYS ALA THR GLY SER SEQRES 25 A 892 ALA SER SER MET ILE ASN GLY VAL VAL LYS LEU LEU THR SEQRES 26 A 892 LYS PRO TRP ASP VAL VAL PRO MET VAL THR GLN MET ALA SEQRES 27 A 892 MET THR ASP THR THR PRO PHE GLY GLN GLN ARG VAL PHE SEQRES 28 A 892 LYS GLU LYS VAL ASP THR ARG THR PRO ARG PRO LEU PRO SEQRES 29 A 892 GLY THR ARG LYS VAL MET GLU ILE THR ALA GLU TRP LEU SEQRES 30 A 892 TRP ARG THR LEU GLY ARG ASN LYS ARG PRO ARG LEU CYS SEQRES 31 A 892 THR ARG GLU GLU PHE THR LYS LYS VAL ARG THR ASN ALA SEQRES 32 A 892 ALA MET GLY ALA VAL PHE THR GLU GLU ASN GLN TRP ASP SEQRES 33 A 892 SER ALA LYS ALA ALA VAL GLU ASP GLU GLU PHE TRP LYS SEQRES 34 A 892 LEU VAL ASP ARG GLU ARG GLU LEU HIS LYS LEU GLY LYS SEQRES 35 A 892 CYS GLY SER CYS VAL TYR ASN MET MET GLY LYS ARG GLU SEQRES 36 A 892 LYS LYS LEU GLY GLU PHE GLY LYS ALA LYS GLY SER ARG SEQRES 37 A 892 ALA ILE TRP TYR MET TRP LEU GLY VAL ARG TYR LEU GLU SEQRES 38 A 892 PHE GLU ALA LEU GLY PHE LEU ASN GLU ASP HIS TRP PHE SEQRES 39 A 892 SER ARG GLU ASN SER TYR SER GLY VAL GLU GLY GLU GLY SEQRES 40 A 892 LEU HIS LYS LEU GLY TYR ILE LEU ARG ASP ILE SER LYS SEQRES 41 A 892 ILE PRO GLY GLY ALA MET TYR ALA ASP ASP THR ALA GLY SEQRES 42 A 892 TRP ASP THR ARG ILE THR GLU ASP ASP LEU HIS ASN GLU SEQRES 43 A 892 GLU LYS ILE ILE GLN GLN MET ASP PRO GLU HIS ARG GLN SEQRES 44 A 892 LEU ALA ASN ALA ILE PHE LYS LEU THR TYR GLN ASN LYS SEQRES 45 A 892 VAL VAL LYS VAL GLN ARG PRO THR PRO THR GLY THR VAL SEQRES 46 A 892 MET ASP ILE ILE SER ARG LYS ASP GLN ARG GLY SER GLY SEQRES 47 A 892 GLN VAL GLY THR TYR GLY LEU ASN THR PHE THR ASN MET SEQRES 48 A 892 GLU ALA GLN LEU VAL ARG GLN MET GLU GLY GLU GLY VAL SEQRES 49 A 892 LEU THR LYS ALA ASP LEU GLU ASN PRO HIS LEU LEU GLU SEQRES 50 A 892 LYS LYS ILE THR GLN TRP LEU GLU THR LYS GLY VAL GLU SEQRES 51 A 892 ARG LEU LYS ARG MET ALA ILE SER GLY ASP ASP CYS VAL SEQRES 52 A 892 VAL LYS PRO ILE ASP ASP ARG PHE ALA ASN ALA LEU LEU SEQRES 53 A 892 ALA LEU ASN ASP MET GLY LYS VAL ARG LYS ASP ILE PRO SEQRES 54 A 892 GLN TRP GLN PRO SER LYS GLY TRP HIS ASP TRP GLN GLN SEQRES 55 A 892 VAL PRO PHE CYS SER HIS HIS PHE HIS GLU LEU ILE MET SEQRES 56 A 892 LYS ASP GLY ARG LYS LEU VAL VAL PRO CYS ARG PRO GLN SEQRES 57 A 892 ASP GLU LEU ILE GLY ARG ALA ARG ILE SER GLN GLY ALA SEQRES 58 A 892 GLY TRP SER LEU ARG GLU THR ALA CYS LEU GLY LYS ALA SEQRES 59 A 892 TYR ALA GLN MET TRP SER LEU MET TYR PHE HIS ARG ARG SEQRES 60 A 892 ASP LEU ARG LEU ALA SER ASN ALA ILE CYS SER ALA VAL SEQRES 61 A 892 PRO VAL HIS TRP VAL PRO THR SER ARG THR THR TRP SER SEQRES 62 A 892 ILE HIS ALA HIS HIS GLN TRP MET THR THR GLU ASP MET SEQRES 63 A 892 LEU THR VAL TRP ASN ARG VAL TRP ILE GLU GLU ASN PRO SEQRES 64 A 892 TRP MET GLU ASP LYS THR PRO VAL THR THR TRP GLU ASN SEQRES 65 A 892 VAL PRO TYR LEU GLY LYS ARG GLU ASP GLN TRP CYS GLY SEQRES 66 A 892 SER LEU ILE GLY LEU THR SER ARG ALA THR TRP ALA GLN SEQRES 67 A 892 ASN ILE PRO THR ALA ILE GLN GLN VAL ARG SER LEU ILE SEQRES 68 A 892 GLY ASN GLU GLU PHE LEU ASP TYR MET PRO SER MET LYS SEQRES 69 A 892 ARG PHE ARG LYS GLU GLU GLU SER HET ZN A1001 1 HET ZN A1002 1 HET SAH A1051 26 HET ACT A1884 4 HET ACT A1885 4 HET ACT A1886 4 HET ACT A1887 4 HET ACT A1888 4 HET ACT A1889 4 HET GOL A1890 6 HETNAM ZN ZINC ION HETNAM SAH S-ADENOSYL-L-HOMOCYSTEINE HETNAM ACT ACETATE ION HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 ZN 2(ZN 2+) FORMUL 4 SAH C14 H20 N6 O5 S FORMUL 5 ACT 6(C2 H3 O2 1-) FORMUL 11 GOL C3 H8 O3 FORMUL 12 HOH *277(H2 O) HELIX 1 1 THR A 8 ASN A 18 1 11 HELIX 2 2 SER A 21 LYS A 29 1 9 HELIX 3 3 ARG A 38 ARG A 47 1 10 HELIX 4 4 ARG A 57 ARG A 68 1 12 HELIX 5 5 GLY A 85 ALA A 92 1 8 HELIX 6 6 GLY A 120 ASN A 122 5 3 HELIX 7 7 ASP A 131 LEU A 135 5 5 HELIX 8 8 SER A 153 GLU A 169 1 17 HELIX 9 9 PRO A 170 LEU A 172 5 3 HELIX 10 10 MET A 186 GLY A 201 1 16 HELIX 11 11 ASN A 226 MET A 244 1 19 HELIX 12 12 HIS A 263 GLU A 267 5 5 HELIX 13 13 ASN A 272 HIS A 287 1 16 HELIX 14 14 ASN A 321 LEU A 326 1 6 HELIX 15 15 THR A 328 ASP A 332 5 5 HELIX 16 16 VAL A 334 GLN A 339 1 6 HELIX 17 17 THR A 346 VAL A 358 1 13 HELIX 18 18 LEU A 366 GLY A 385 1 20 HELIX 19 19 THR A 394 THR A 404 1 11 HELIX 20 20 TRP A 418 VAL A 425 1 8 HELIX 21 21 ASP A 427 LEU A 443 1 17 HELIX 22 22 SER A 470 GLY A 489 1 20 HELIX 23 23 GLY A 489 ASP A 494 1 6 HELIX 24 24 SER A 498 TYR A 503 1 6 HELIX 25 25 GLY A 510 LYS A 523 1 14 HELIX 26 26 GLY A 536 ILE A 541 5 6 HELIX 27 27 THR A 542 GLU A 550 1 9 HELIX 28 28 LYS A 551 MET A 556 5 6 HELIX 29 29 ASP A 557 THR A 571 1 15 HELIX 30 30 GLY A 604 GLU A 625 1 22 HELIX 31 31 THR A 629 ASN A 635 1 7 HELIX 32 32 GLU A 640 LYS A 656 1 17 HELIX 33 33 ASP A 671 ALA A 677 5 7 HELIX 34 34 LEU A 678 MET A 684 1 7 HELIX 35 35 ASP A 702 VAL A 706 5 5 HELIX 36 36 PRO A 730 ARG A 739 1 10 HELIX 37 37 LEU A 748 TYR A 766 1 19 HELIX 38 38 ARG A 769 ALA A 782 1 14 HELIX 39 39 ASP A 808 ILE A 818 1 11 HELIX 40 40 THR A 832 VAL A 836 5 5 HELIX 41 41 GLY A 840 CYS A 847 1 8 HELIX 42 42 LEU A 853 ASN A 862 1 10 HELIX 43 43 ASN A 862 GLY A 875 1 14 SHEET 1 AA 2 THR A 34 VAL A 36 0 SHEET 2 AA 2 THR A 250 GLU A 252 1 O THR A 250 N GLU A 35 SHEET 1 AB 7 VAL A 124 MET A 127 0 SHEET 2 AB 7 VAL A 97 TYR A 103 1 O VAL A 100 N LYS A 125 SHEET 3 AB 7 GLY A 75 LEU A 80 1 O GLY A 75 N THR A 98 SHEET 4 AB 7 THR A 142 CYS A 145 1 O THR A 142 N ILE A 78 SHEET 5 AB 7 GLN A 176 VAL A 181 1 O GLN A 176 N LEU A 143 SHEET 6 AB 7 MET A 217 ILE A 220 -1 O MET A 217 N VAL A 181 SHEET 7 AB 7 MET A 203 VAL A 205 -1 O MET A 203 N ILE A 220 SHEET 1 AC 4 ALA A 303 GLU A 309 0 SHEET 2 AC 4 GLY A 586 ARG A 594 -1 O MET A 589 N TYR A 308 SHEET 3 AC 4 LYS A 575 THR A 583 -1 O LYS A 575 N ARG A 594 SHEET 4 AC 4 TYR A 451 ASN A 452 1 O TYR A 451 N LYS A 578 SHEET 1 AD 2 MET A 658 SER A 661 0 SHEET 2 AD 2 ASP A 664 VAL A 667 -1 O ASP A 664 N SER A 661 SHEET 1 AE 2 HIS A 712 ILE A 717 0 SHEET 2 AE 2 LYS A 723 CYS A 728 -1 O LEU A 724 N LEU A 716 LINK OE2 GLU A 437 ZN ZN A1001 1555 1555 2.24 LINK NE2 HIS A 441 ZN ZN A1001 1555 1555 2.04 LINK SG CYS A 446 ZN ZN A1001 1555 1555 2.50 LINK SG CYS A 449 ZN ZN A1001 1555 1555 2.03 LINK NE2 HIS A 712 ZN ZN A1002 1555 1555 2.10 LINK SG CYS A 728 ZN ZN A1002 1555 1555 2.43 LINK SG CYS A 847 ZN ZN A1002 1555 1555 2.48 SITE 1 AC1 4 GLU A 437 HIS A 441 CYS A 446 CYS A 449 SITE 1 AC2 4 HIS A 712 HIS A 714 CYS A 728 CYS A 847 SITE 1 AC3 17 SER A 56 GLY A 58 GLY A 81 CYS A 82 SITE 2 AC3 17 GLY A 86 TRP A 87 LYS A 105 HIS A 110 SITE 3 AC3 17 GLU A 111 LYS A 130 ASP A 131 VAL A 132 SITE 4 AC3 17 PHE A 133 ASP A 146 HOH A2042 HOH A2044 SITE 5 AC3 17 HOH A2061 SITE 1 AC4 4 ARG A 57 LYS A 61 LEU A 209 HOH A2030 SITE 1 AC5 3 ARG A 38 LYS A 42 HOH A2027 SITE 1 AC6 3 LYS A 14 ASN A 18 SER A 213 SITE 1 AC7 1 HIS A 52 SITE 1 AC8 4 GLU A 112 SER A 522 LYS A 668 HIS A 701 SITE 1 AC9 1 HOH A2073 SITE 1 BC1 6 ASP A 256 GLY A 258 LYS A 300 LYS A 355 SITE 2 BC1 6 GLU A 356 ASP A 359 CRYST1 95.129 151.445 69.124 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 0.010512 0.000000 0.000000 0.00000 SCALE2 0.000000 0.006603 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014467 0.00000