HEADER VIRAL PROTEIN/RNA 18-SEP-15 5DTO TITLE DENGUE VIRUS FULL LENGTH NS5 COMPLEXED WITH VIRAL CAP 0-RNA AND SAH COMPND MOL_ID: 1; COMPND 2 MOLECULE: NS5; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 2496-3385; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: RNA (5'-R(P*AP*GP*UP*U)-3'); COMPND 8 CHAIN: B; COMPND 9 ENGINEERED: YES; COMPND 10 OTHER_DETAILS: CAP0 VIRAL RNA SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DENGUE VIRUS 3; SOURCE 3 ORGANISM_TAXID: 11069; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)-RIL; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PNIC28-BSA4; SOURCE 9 MOL_ID: 2; SOURCE 10 SYNTHETIC: YES; SOURCE 11 ORGANISM_SCIENTIFIC: DENGUE VIRUS; SOURCE 12 ORGANISM_TAXID: 12637 KEYWDS DENGUE VIRUS, NONSTRUCTURAL PROTEIN 5, 2'OMTASE, CAP0 RNA, INNATE KEYWDS 2 IMMUNITY EVASION, VIRAL PROTEIN-RNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR Y.ZHAO,T.S.SOH,S.P.LIM,K.Y.CHUNG,K.SWAMINATHAN,S.G.VASUDEVAN,P.- AUTHOR 2 Y.SHI,J.LESCAR,D.LUO REVDAT 4 06-MAR-24 5DTO 1 COMPND JRNL REMARK FORMUL REVDAT 4 2 1 LINK REVDAT 3 16-DEC-15 5DTO 1 JRNL REVDAT 2 02-DEC-15 5DTO 1 JRNL REVDAT 1 25-NOV-15 5DTO 0 JRNL AUTH Y.ZHAO,T.S.SOH,S.P.LIM,K.Y.CHUNG,K.SWAMINATHAN, JRNL AUTH 2 S.G.VASUDEVAN,P.-Y.SHI,J.LESCAR,D.LUO JRNL TITL MOLECULAR BASIS FOR SPECIFIC VIRAL RNA RECOGNITION AND JRNL TITL 2 2'-O-RIBOSE METHYLATION BY THE DENGUE VIRUS NONSTRUCTURAL JRNL TITL 3 PROTEIN 5 (NS5) JRNL REF PROC.NATL.ACAD.SCI.USA V. 112 14834 2015 JRNL REFN ESSN 1091-6490 JRNL PMID 26578813 JRNL DOI 10.1073/PNAS.1514978112 REMARK 2 REMARK 2 RESOLUTION. 2.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.9_1692 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) : 2.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.33 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 31264 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.186 REMARK 3 R VALUE (WORKING SET) : 0.183 REMARK 3 FREE R VALUE : 0.244 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.040 REMARK 3 FREE R VALUE TEST SET COUNT : 1576 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 47.3378 - 5.7848 1.00 2892 134 0.1686 0.2000 REMARK 3 2 5.7848 - 4.5928 1.00 2742 158 0.1553 0.2189 REMARK 3 3 4.5928 - 4.0126 1.00 2715 154 0.1412 0.1987 REMARK 3 4 4.0126 - 3.6459 1.00 2695 131 0.1619 0.2139 REMARK 3 5 3.6459 - 3.3846 1.00 2694 156 0.1739 0.2385 REMARK 3 6 3.3846 - 3.1851 1.00 2657 153 0.1969 0.2818 REMARK 3 7 3.1851 - 3.0256 1.00 2679 139 0.2076 0.2875 REMARK 3 8 3.0256 - 2.8940 1.00 2649 159 0.2241 0.2721 REMARK 3 9 2.8940 - 2.7826 1.00 2666 144 0.2390 0.3215 REMARK 3 10 2.7826 - 2.6866 1.00 2659 128 0.2485 0.3733 REMARK 3 11 2.6866 - 2.6026 0.98 2640 120 0.2857 0.3382 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) : 0.350 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.750 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 : 0.003 7167 REMARK 3 ANGLE : 0.779 9723 REMARK 3 CHIRALITY : 0.032 1045 REMARK 3 PLANARITY : 0.004 1223 REMARK 3 DIHEDRAL : 13.366 2686 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 6 THROUGH 334 ) REMARK 3 ORIGIN FOR THE GROUP (A): 29.8845 140.2227 13.0353 REMARK 3 T TENSOR REMARK 3 T11: 0.2397 T22: 0.2693 REMARK 3 T33: 0.2376 T12: 0.0294 REMARK 3 T13: -0.0489 T23: -0.0222 REMARK 3 L TENSOR REMARK 3 L11: 0.8287 L22: 1.7396 REMARK 3 L33: 0.4280 L12: -0.1145 REMARK 3 L13: 0.0644 L23: -0.0132 REMARK 3 S TENSOR REMARK 3 S11: 0.0097 S12: -0.1706 S13: 0.0141 REMARK 3 S21: 0.2482 S22: 0.0279 S23: -0.2507 REMARK 3 S31: 0.0485 S32: 0.0360 S33: -0.0429 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 335 THROUGH 688 ) REMARK 3 ORIGIN FOR THE GROUP (A): 18.3201 172.9178 -2.7122 REMARK 3 T TENSOR REMARK 3 T11: 0.2217 T22: 0.2132 REMARK 3 T33: 0.2127 T12: -0.0033 REMARK 3 T13: -0.0306 T23: 0.0164 REMARK 3 L TENSOR REMARK 3 L11: 1.5914 L22: 1.0384 REMARK 3 L33: 0.5304 L12: -0.1855 REMARK 3 L13: -0.3516 L23: -0.1550 REMARK 3 S TENSOR REMARK 3 S11: -0.0730 S12: -0.0683 S13: 0.0149 REMARK 3 S21: -0.0634 S22: -0.0491 S23: -0.1068 REMARK 3 S31: -0.0048 S32: 0.1464 S33: 0.1006 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 689 THROUGH 883 ) REMARK 3 ORIGIN FOR THE GROUP (A): 17.5395 180.5355 26.9601 REMARK 3 T TENSOR REMARK 3 T11: 0.4676 T22: 0.6727 REMARK 3 T33: 0.3779 T12: -0.0911 REMARK 3 T13: -0.0297 T23: -0.0162 REMARK 3 L TENSOR REMARK 3 L11: 1.1825 L22: 0.8974 REMARK 3 L33: 2.1379 L12: 0.0330 REMARK 3 L13: 0.5306 L23: 0.0023 REMARK 3 S TENSOR REMARK 3 S11: -0.0023 S12: -0.4336 S13: 0.1806 REMARK 3 S21: 0.2158 S22: -0.1247 S23: -0.1699 REMARK 3 S31: -0.3961 S32: 0.4529 S33: 0.1313 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 0 THROUGH 4 ) REMARK 3 ORIGIN FOR THE GROUP (A): 21.939 134.871 26.069 REMARK 3 T TENSOR REMARK 3 T11: 0.8900 T22: 0.9198 REMARK 3 T33: 1.0874 T12: 0.1259 REMARK 3 T13: 0.0161 T23: -0.1952 REMARK 3 L TENSOR REMARK 3 L11: 1.5708 L22: 1.0007 REMARK 3 L33: 3.0835 L12: 0.3372 REMARK 3 L13: 1.5835 L23: -0.8361 REMARK 3 S TENSOR REMARK 3 S11: -0.0051 S12: -0.0862 S13: 0.2856 REMARK 3 S21: 0.3527 S22: -0.0201 S23: 0.6013 REMARK 3 S31: -0.0405 S32: -0.5686 S33: 0.0205 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 5DTO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 24-SEP-15. REMARK 100 THE DEPOSITION ID IS D_1000213457. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-MAY-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.4 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06DA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 31340 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.603 REMARK 200 RESOLUTION RANGE LOW (A) : 47.330 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 5.900 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 1.3500 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: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.32 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.38 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M MAGNESIUM ACETATE, 0.1 M SODIUM REMARK 280 CACODYLATE, 10-20%(W/V) PEG 8000, PH 6.4, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 291K 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 47.33000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 75.69700 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 47.33000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 75.69700 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: 2160 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 36650 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -38.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 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 A1320 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 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 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 SER A 470 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 GLN A 417 CG CD OE1 NE2 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 ILE A 748 CG1 CG2 CD1 REMARK 470 ARG A 749 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 750 CG CD OE1 OE2 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: 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 -41.22 66.63 REMARK 500 LYS A 173 85.63 -155.12 REMARK 500 GLN A 339 -24.83 -155.04 REMARK 500 ASN A 405 40.40 -51.94 REMARK 500 SER A 448 39.27 -143.46 REMARK 500 ALA A 472 78.62 -64.24 REMARK 500 TYR A 503 -53.10 61.21 REMARK 500 VAL A 506 29.66 -141.32 REMARK 500 GLU A 509 -61.23 -96.68 REMARK 500 ASP A 596 -153.54 -94.77 REMARK 500 GLN A 597 174.03 64.52 REMARK 500 GLN A 742 66.94 -158.98 REMARK 500 ARG A 749 21.70 -73.25 REMARK 500 GLU A 750 -26.66 -143.28 REMARK 500 SER A 791 146.60 65.74 REMARK 500 THR A 793 -70.98 -67.60 REMARK 500 TRP A 795 31.77 -91.27 REMARK 500 ILE A 818 -75.99 -117.41 REMARK 500 ILE A 874 -71.18 -76.92 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 95.7 REMARK 620 3 CYS A 446 SG 106.9 115.4 REMARK 620 4 CYS A 449 SG 114.5 118.8 105.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A1004 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 533 OD1 REMARK 620 2 ASP A 664 OD1 77.5 REMARK 620 3 HOH A1144 O 62.1 68.9 REMARK 620 4 HOH A1145 O 126.1 83.1 64.1 REMARK 620 5 HOH A1160 O 75.8 130.7 62.1 80.4 REMARK 620 6 HOH A1301 O 109.7 110.1 171.7 124.2 117.6 REMARK 620 N 1 2 3 4 5 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 HIS A 714 NE2 107.9 REMARK 620 3 CYS A 728 SG 113.8 105.5 REMARK 620 4 CYS A 847 SG 102.5 111.5 115.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 102 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 M7G B 0 O1A REMARK 620 2 M7G B 0 O2B 88.1 REMARK 620 3 A B 1 OP1 87.9 90.5 REMARK 620 4 HOH B 201 O 177.9 90.7 93.8 REMARK 620 5 HOH B 205 O 91.8 90.5 179.0 86.5 REMARK 620 6 HOH B 207 O 91.2 179.2 89.3 90.1 89.7 REMARK 620 N 1 2 3 4 5 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 1003 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 1004 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT A 1005 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue M7G B 0 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG B 102 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 REMARK 900 RELATED ID: 4V0Q RELATED DB: PDB REMARK 900 DENGUE VIRUS FULL LENGTH NS5 COMPLEXED WITH SAH DBREF 5DTO A 6 895 UNP A1XTB9 A1XTB9_9FLAV 2496 3385 DBREF 5DTO B 1 4 PDB 5DTO 5DTO 1 4 SEQADV 5DTO SER A 4 UNP A1XTB9 EXPRESSION TAG SEQADV 5DTO MET A 5 UNP A1XTB9 EXPRESSION TAG SEQADV 5DTO ILE A 72 UNP A1XTB9 VAL 2562 CONFLICT SEQADV 5DTO LEU A 366 UNP A1XTB9 MET 2856 CONFLICT SEQADV 5DTO VAL A 480 UNP A1XTB9 ALA 2970 CONFLICT SEQADV 5DTO ILE A 748 UNP A1XTB9 LEU 3238 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 ILE 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 SEQRES 1 B 4 A G U U HET ZN A1001 1 HET ZN A1002 1 HET SAH A1003 26 HET MG A1004 1 HET ACT A1005 4 HET M7G B 0 29 HET MG B 102 1 HETNAM ZN ZINC ION HETNAM SAH S-ADENOSYL-L-HOMOCYSTEINE HETNAM MG MAGNESIUM ION HETNAM ACT ACETATE ION HETNAM M7G 7N-METHYL-8-HYDROGUANOSINE-5'-DIPHOSPHATE FORMUL 3 ZN 2(ZN 2+) FORMUL 5 SAH C14 H20 N6 O5 S FORMUL 6 MG 2(MG 2+) FORMUL 7 ACT C2 H3 O2 1- FORMUL 8 M7G C11 H18 N5 O11 P2 1+ FORMUL 10 HOH *241(H2 O) HELIX 1 AA1 THR A 8 ASN A 18 1 11 HELIX 2 AA2 SER A 21 LYS A 29 1 9 HELIX 3 AA3 ARG A 38 ARG A 47 1 10 HELIX 4 AA4 ARG A 57 ARG A 68 1 12 HELIX 5 AA5 GLY A 85 ALA A 92 1 8 HELIX 6 AA6 GLY A 120 ASN A 122 5 3 HELIX 7 AA7 ASP A 131 LEU A 135 5 5 HELIX 8 AA8 SER A 153 GLU A 169 1 17 HELIX 9 AA9 PRO A 170 LEU A 172 5 3 HELIX 10 AB1 MET A 186 GLY A 201 1 16 HELIX 11 AB2 ASN A 226 MET A 244 1 19 HELIX 12 AB3 HIS A 263 GLU A 267 5 5 HELIX 13 AB4 ASN A 272 HIS A 287 1 16 HELIX 14 AB5 ASN A 321 THR A 328 1 8 HELIX 15 AB6 LYS A 329 VAL A 333 5 5 HELIX 16 AB7 THR A 346 VAL A 358 1 13 HELIX 17 AB8 LEU A 366 GLY A 385 1 20 HELIX 18 AB9 THR A 394 THR A 404 1 11 HELIX 19 AC1 ASP A 419 ASP A 427 1 9 HELIX 20 AC2 ASP A 427 LEU A 443 1 17 HELIX 21 AC3 ILE A 473 GLY A 489 1 17 HELIX 22 AC4 GLY A 489 ASP A 494 1 6 HELIX 23 AC5 SER A 498 TYR A 503 1 6 HELIX 24 AC6 GLY A 510 LYS A 523 1 14 HELIX 25 AC7 GLY A 536 ILE A 541 5 6 HELIX 26 AC8 THR A 542 GLU A 550 1 9 HELIX 27 AC9 LYS A 551 MET A 556 5 6 HELIX 28 AD1 ASP A 557 TYR A 572 1 16 HELIX 29 AD2 GLY A 604 GLU A 625 1 22 HELIX 30 AD3 THR A 629 ASN A 635 1 7 HELIX 31 AD4 GLU A 640 LYS A 656 1 17 HELIX 32 AD5 ASP A 672 ASN A 676 5 5 HELIX 33 AD6 LEU A 678 MET A 684 1 7 HELIX 34 AD7 ASP A 702 VAL A 706 5 5 HELIX 35 AD8 PRO A 730 ARG A 739 1 10 HELIX 36 AD9 SER A 747 TYR A 766 1 20 HELIX 37 AE1 ARG A 769 SER A 781 1 13 HELIX 38 AE2 ASP A 808 ILE A 818 1 11 HELIX 39 AE3 GLY A 840 CYS A 847 1 8 HELIX 40 AE4 LEU A 853 GLN A 861 1 9 HELIX 41 AE5 ASN A 862 GLY A 875 1 14 SHEET 1 AA1 2 THR A 34 VAL A 36 0 SHEET 2 AA1 2 THR A 250 GLU A 252 1 O THR A 250 N GLU A 35 SHEET 1 AA2 7 VAL A 124 MET A 127 0 SHEET 2 AA2 7 VAL A 97 TYR A 103 1 N GLY A 102 O LYS A 125 SHEET 3 AA2 7 GLY A 75 LEU A 80 1 N VAL A 77 O GLU A 99 SHEET 4 AA2 7 THR A 142 CYS A 145 1 O LEU A 144 N ILE A 78 SHEET 5 AA2 7 GLN A 176 VAL A 181 1 O GLN A 176 N LEU A 143 SHEET 6 AA2 7 MET A 217 ILE A 220 -1 O MET A 217 N VAL A 181 SHEET 7 AA2 7 MET A 203 VAL A 205 -1 N VAL A 205 O TYR A 218 SHEET 1 AA3 4 ALA A 303 VAL A 310 0 SHEET 2 AA3 4 GLY A 586 ARG A 594 -1 O MET A 589 N TYR A 308 SHEET 3 AA3 4 LYS A 575 THR A 583 -1 N VAL A 579 O ASP A 590 SHEET 4 AA3 4 TYR A 451 MET A 453 1 N TYR A 451 O LYS A 578 SHEET 1 AA4 2 MET A 658 SER A 661 0 SHEET 2 AA4 2 ASP A 664 VAL A 667 -1 O ASP A 664 N SER A 661 SHEET 1 AA5 2 HIS A 712 ILE A 717 0 SHEET 2 AA5 2 LYS A 723 CYS A 728 -1 O LEU A 724 N LEU A 716 LINK O1B M7G B 0 P A B 1 1555 1555 1.60 LINK OE2 GLU A 437 ZN ZN A1001 1555 1555 2.00 LINK NE2 HIS A 441 ZN ZN A1001 1555 1555 2.05 LINK SG CYS A 446 ZN ZN A1001 1555 1555 2.39 LINK SG CYS A 449 ZN ZN A1001 1555 1555 2.16 LINK OD1 ASP A 533 MG MG A1004 1555 1555 2.59 LINK OD1 ASP A 664 MG MG A1004 1555 1555 2.16 LINK NE2 HIS A 712 ZN ZN A1002 1555 1555 2.02 LINK NE2 HIS A 714 ZN ZN A1002 1555 1555 1.99 LINK SG CYS A 728 ZN ZN A1002 1555 1555 2.39 LINK SG CYS A 847 ZN ZN A1002 1555 1555 2.30 LINK MG MG A1004 O HOH A1144 1555 1555 2.32 LINK MG MG A1004 O HOH A1145 1555 1555 2.38 LINK MG MG A1004 O HOH A1160 1555 1555 2.19 LINK MG MG A1004 O HOH A1301 1555 1555 2.86 LINK O1A M7G B 0 MG MG B 102 1555 1555 1.98 LINK O2B M7G B 0 MG MG B 102 1555 1555 2.02 LINK OP1 A B 1 MG MG B 102 1555 1555 2.06 LINK MG MG B 102 O HOH B 201 1555 1555 2.00 LINK MG MG B 102 O HOH B 205 1555 1555 2.01 LINK MG MG B 102 O HOH B 207 1555 1555 2.02 CISPEP 1 GLN A 742 GLY A 743 0 -1.68 CISPEP 2 GLY A 745 TRP A 746 0 -2.01 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 22 SER A 56 GLY A 58 GLY A 81 CYS A 82 SITE 2 AC3 22 GLY A 85 GLY A 86 TRP A 87 THR A 104 SITE 3 AC3 22 LYS A 105 HIS A 110 GLU A 111 LYS A 130 SITE 4 AC3 22 ASP A 131 VAL A 132 PHE A 133 ASP A 146 SITE 5 AC3 22 HOH A1118 HOH A1255 A B 1 G B 2 SITE 6 AC3 22 HOH B 202 HOH B 211 SITE 1 AC4 6 ASP A 533 ASP A 664 HOH A1144 HOH A1145 SITE 2 AC4 6 HOH A1160 HOH A1301 SITE 1 AC5 4 GLU A 428 ARG A 499 LYS A 656 HOH A1246 SITE 1 AC6 18 LYS A 14 LEU A 17 ASN A 18 LEU A 20 SITE 2 AC6 18 PHE A 25 LYS A 29 SER A 151 PRO A 152 SITE 3 AC6 18 ARG A 211 SER A 213 THR A 214 A B 1 SITE 4 AC6 18 MG B 102 HOH B 201 HOH B 203 HOH B 204 SITE 5 AC6 18 HOH B 205 HOH B 207 SITE 1 AC7 5 M7G B 0 A B 1 HOH B 201 HOH B 205 SITE 2 AC7 5 HOH B 207 CRYST1 94.660 151.394 69.432 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 0.010564 0.000000 0.000000 0.00000 SCALE2 0.000000 0.006605 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014403 0.00000