HEADER VIRAL PROTEIN 05-AUG-18 6H9R TITLE DENGUE-RDRP3-INHIBITOR COMPLEX SOAKING COMPND MOL_ID: 1; COMPND 2 MOLECULE: GENOME POLYPROTEIN; COMPND 3 CHAIN: A; COMPND 4 EC: 3.4.21.91,3.6.1.15,3.6.4.13,2.1.1.56,2.1.1.57,2.7.7.48; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DENGUE VIRUS 3 SRI LANKA/1266/2000; SOURCE 3 ORGANISM_TAXID: 408692; SOURCE 4 GENE: POL; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI 'BL21-GOLD(DE3)PLYSS AG'; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 866768 KEYWDS DENGUE VIRUS; CRYSTALLIZATION SCREEN; RNA-DEPENDENT RNA POLYMERASE; KEYWDS 2 FLAVIVIRUS; ANTIVIRAL DRUG-DISCOVERY, VIRAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR S.K.TALAPATRA,F.KOZIELSKI REVDAT 2 17-JAN-24 6H9R 1 REMARK REVDAT 1 13-MAR-19 6H9R 0 JRNL AUTH F.RICCIO,S.K.TALAPATRA,S.OXENFORD,R.ANGELL,M.MAZZON, JRNL AUTH 2 F.KOZIELSKI JRNL TITL DEVELOPMENT AND VALIDATION OF RDRP SCREEN, A CRYSTALLIZATION JRNL TITL 2 SCREEN FOR VIRAL RNA-DEPENDENT RNA POLYMERASES. JRNL REF BIOL OPEN V. 8 2019 JRNL REFN ESSN 2046-6390 JRNL PMID 30602529 JRNL DOI 10.1242/BIO.037663 REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.13_2998: ???) 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.79 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 34089 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.200 REMARK 3 R VALUE (WORKING SET) : 0.198 REMARK 3 FREE R VALUE : 0.248 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.170 REMARK 3 FREE R VALUE TEST SET COUNT : 1763 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 48.7988 - 5.6405 1.00 2677 136 0.1803 0.2355 REMARK 3 2 5.6405 - 4.4781 1.00 2535 151 0.1696 0.2037 REMARK 3 3 4.4781 - 3.9123 0.99 2515 139 0.1699 0.1959 REMARK 3 4 3.9123 - 3.5547 0.90 2270 131 0.2316 0.2921 REMARK 3 5 3.5547 - 3.3000 0.99 2490 131 0.2077 0.2438 REMARK 3 6 3.3000 - 3.1054 1.00 2500 150 0.2002 0.2766 REMARK 3 7 3.1054 - 2.9499 1.00 2480 138 0.1960 0.2732 REMARK 3 8 2.9499 - 2.8215 1.00 2491 138 0.2027 0.2484 REMARK 3 9 2.8215 - 2.7129 1.00 2453 147 0.2090 0.2708 REMARK 3 10 2.7129 - 2.6193 1.00 2492 122 0.2022 0.2549 REMARK 3 11 2.6193 - 2.5374 1.00 2481 121 0.2222 0.2720 REMARK 3 12 2.5374 - 2.4649 1.00 2484 130 0.2454 0.3100 REMARK 3 13 2.4649 - 2.4000 1.00 2458 129 0.2805 0.3370 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.270 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.700 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 : 0.012 4692 REMARK 3 ANGLE : 1.200 6350 REMARK 3 CHIRALITY : 0.061 672 REMARK 3 PLANARITY : 0.007 809 REMARK 3 DIHEDRAL : 7.887 3809 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 6H9R COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 05-AUG-18. REMARK 100 THE DEPOSITION ID IS D_1200011229. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-APR-16 REMARK 200 TEMPERATURE (KELVIN) : 80 REMARK 200 PH : 8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I03 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.98 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 34409 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 48.800 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 2.000 REMARK 200 R MERGE (I) : 0.05300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.6000 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 (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.46400 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 REMARK 200 STARTING MODEL: 4HHJ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 58.45 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.96 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M TRIS PH 8.0, 22% PEG 550 MME, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 28.95000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 28.95000 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 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 82.34550 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 90.60500 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 82.34550 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 90.60500 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 28.95000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 82.34550 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 90.60500 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 28.95000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 82.34550 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 90.60500 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1520 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 25060 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 16.0 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 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 GLY A 266 REMARK 465 SER A 267 REMARK 465 HIS A 268 REMARK 465 MET A 269 REMARK 465 LEU A 270 REMARK 465 ASP A 271 REMARK 465 ALA A 312 REMARK 465 THR A 313 REMARK 465 GLY A 314 REMARK 465 SER A 315 REMARK 465 ALA A 316 REMARK 465 SER A 317 REMARK 465 SER A 318 REMARK 465 THR A 343 REMARK 465 ASP A 344 REMARK 465 THR A 345 REMARK 465 THR A 346 REMARK 465 PRO A 347 REMARK 465 PHE A 348 REMARK 465 GLY A 349 REMARK 465 GLN A 350 REMARK 465 GLN A 351 REMARK 465 ARG A 352 REMARK 465 VAL A 353 REMARK 465 PHE A 354 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 TRP A 418 REMARK 465 MET A 454 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 ARG A 581 REMARK 465 PRO A 582 REMARK 465 THR A 583 REMARK 465 PRO A 584 REMARK 465 THR A 585 REMARK 465 GLY A 586 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 465 GLU A 896 REMARK 465 GLY A 897 REMARK 465 ALA A 898 REMARK 465 ILE A 899 REMARK 465 TRP A 900 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 ASP A 274 OD1 OD2 REMARK 470 GLU A 278 CG CD OE1 OE2 REMARK 470 LYS A 281 CD CE NZ REMARK 470 SER A 289 OG REMARK 470 ASP A 295 CG OD1 OD2 REMARK 470 GLU A 296 CG CD OE1 OE2 REMARK 470 LYS A 300 CG CD CE NZ REMARK 470 VAL A 310 CG1 CG2 REMARK 470 LYS A 311 CG CD CE NZ REMARK 470 MET A 319 CG SD CE REMARK 470 LYS A 355 CE NZ REMARK 470 LYS A 357 CG CD CE NZ REMARK 470 LYS A 400 CG CD CE NZ REMARK 470 ASP A 419 CG OD1 OD2 REMARK 470 LYS A 422 CG CD CE NZ REMARK 470 LYS A 432 CG CD CE NZ REMARK 470 LYS A 445 CD CE NZ REMARK 470 TYR A 451 CD1 CD2 CE1 CE2 CZ OH REMARK 470 ARG A 471 CG CD NE CZ NH1 NH2 REMARK 470 VAL A 480 CG1 CG2 REMARK 470 GLN A 580 CG CD OE1 NE2 REMARK 470 LYS A 641 CG CD CE NZ REMARK 470 GLN A 645 CD OE1 NE2 REMARK 470 LYS A 698 CG CD CE NZ REMARK 470 GLU A 834 CD OE1 OE2 REMARK 470 LYS A 841 CG CD CE NZ 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 ND1 HIS A 701 O HOH A 1101 1.75 REMARK 500 ND1 HIS A 495 O HOH A 1102 1.81 REMARK 500 O HOH A 1273 O HOH A 1279 1.89 REMARK 500 O HOH A 1138 O HOH A 1277 1.95 REMARK 500 O LEU A 639 O HOH A 1103 2.00 REMARK 500 O HOH A 1148 O HOH A 1243 2.00 REMARK 500 O ILE A 591 O HOH A 1104 2.01 REMARK 500 O HOH A 1220 O HOH A 1259 2.04 REMARK 500 O HOH A 1202 O HOH A 1240 2.05 REMARK 500 OE1 GLU A 819 O HOH A 1105 2.07 REMARK 500 O1 PEG A 1007 O HOH A 1106 2.09 REMARK 500 NH2 ARG A 389 O HOH A 1107 2.11 REMARK 500 OE1 GLU A 507 O HOH A 1102 2.15 REMARK 500 OE1 GLU A 640 O HOH A 1108 2.18 REMARK 500 O HIS A 512 O HOH A 1109 2.18 REMARK 500 NH1 ARG A 481 O HOH A 1110 2.18 REMARK 500 OD2 ASP A 702 O HOH A 1111 2.18 REMARK 500 CE1 HIS A 701 O HOH A 1101 2.18 REMARK 500 OD1 ASP A 683 O HOH A 1112 2.18 REMARK 500 OD1 ASP A 732 O HOH A 1113 2.19 REMARK 500 NZ LYS A 650 O HOH A 1114 2.19 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 O2 PEG A 1011 O2 PEG A 1011 4554 0.55 REMARK 500 O2 PEG A 1011 C3 PEG A 1011 4554 1.78 REMARK 500 O HOH A 1194 O HOH A 1263 6555 2.15 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 THR A 290 39.56 -144.34 REMARK 500 PRO A 298 40.75 -93.51 REMARK 500 VAL A 333 -74.71 -38.27 REMARK 500 VAL A 334 125.30 -37.00 REMARK 500 SER A 448 23.42 -151.29 REMARK 500 ALA A 472 -0.68 57.34 REMARK 500 TYR A 503 -52.00 69.10 REMARK 500 ALA A 528 174.65 -58.54 REMARK 500 ASN A 574 78.31 -162.03 REMARK 500 ASP A 596 -158.08 -143.33 REMARK 500 GLN A 597 174.64 62.19 REMARK 500 SER A 600 -77.70 -53.99 REMARK 500 GLN A 602 130.20 5.20 REMARK 500 SER A 791 148.73 61.67 REMARK 500 ILE A 818 -71.09 -117.78 REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 PEG A 1011 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 A1002 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 437 OE1 REMARK 620 2 HIS A 441 NE2 103.3 REMARK 620 3 CYS A 446 SG 94.6 114.4 REMARK 620 4 CYS A 449 SG 121.2 108.4 114.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1003 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 712 NE2 REMARK 620 2 HIS A 714 NE2 91.9 REMARK 620 3 CYS A 728 SG 107.5 112.4 REMARK 620 4 CYS A 847 SG 103.6 117.7 118.9 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 5V5 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 ZN A 1003 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PEG A 1004 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PEG A 1005 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PEG A 1006 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PEG A 1007 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PEG A 1008 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PEG A 1009 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PEG A 1010 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PEG A 1011 DBREF 6H9R A 272 900 UNP Q6YMS4 POLG_DEN3S 2762 3390 SEQADV 6H9R GLY A 266 UNP Q6YMS4 EXPRESSION TAG SEQADV 6H9R SER A 267 UNP Q6YMS4 EXPRESSION TAG SEQADV 6H9R HIS A 268 UNP Q6YMS4 EXPRESSION TAG SEQADV 6H9R MET A 269 UNP Q6YMS4 EXPRESSION TAG SEQADV 6H9R LEU A 270 UNP Q6YMS4 EXPRESSION TAG SEQADV 6H9R ASP A 271 UNP Q6YMS4 EXPRESSION TAG SEQADV 6H9R LEU A 366 UNP Q6YMS4 MET 2856 VARIANT SEQADV 6H9R VAL A 372 UNP Q6YMS4 ALA 2862 VARIANT SEQADV 6H9R VAL A 480 UNP Q6YMS4 ALA 2970 VARIANT SEQADV 6H9R VAL A 603 UNP Q6YMS4 LEU 3093 VARIANT SEQRES 1 A 635 GLY SER HIS MET LEU ASP ASN MET ASP VAL ILE GLY GLU SEQRES 2 A 635 ARG ILE LYS ARG ILE LYS GLU GLU HIS ASN SER THR TRP SEQRES 3 A 635 HIS TYR ASP ASP GLU ASN PRO TYR LYS THR TRP ALA TYR SEQRES 4 A 635 HIS GLY SER TYR GLU VAL LYS ALA THR GLY SER ALA SER SEQRES 5 A 635 SER MET ILE ASN GLY VAL VAL LYS LEU LEU THR LYS PRO SEQRES 6 A 635 TRP ASP VAL VAL PRO MET VAL THR GLN MET ALA MET THR SEQRES 7 A 635 ASP THR THR PRO PHE GLY GLN GLN ARG VAL PHE LYS GLU SEQRES 8 A 635 LYS VAL ASP THR ARG THR PRO ARG PRO LEU PRO GLY THR SEQRES 9 A 635 ARG LYS VAL MET GLU ILE THR ALA GLU TRP LEU TRP ARG SEQRES 10 A 635 THR LEU GLY ARG ASN LYS ARG PRO ARG LEU CYS THR ARG SEQRES 11 A 635 GLU GLU PHE THR LYS LYS VAL ARG THR ASN ALA ALA MET SEQRES 12 A 635 GLY ALA VAL PHE THR GLU GLU ASN GLN TRP ASP SER ALA SEQRES 13 A 635 LYS ALA ALA VAL GLU ASP GLU GLU PHE TRP LYS LEU VAL SEQRES 14 A 635 ASP ARG GLU ARG GLU LEU HIS LYS LEU GLY LYS CYS GLY SEQRES 15 A 635 SER CYS VAL TYR ASN MET MET GLY LYS ARG GLU LYS LYS SEQRES 16 A 635 LEU GLY GLU PHE GLY LYS ALA LYS GLY SER ARG ALA ILE SEQRES 17 A 635 TRP TYR MET TRP LEU GLY VAL ARG TYR LEU GLU PHE GLU SEQRES 18 A 635 ALA LEU GLY PHE LEU ASN GLU ASP HIS TRP PHE SER ARG SEQRES 19 A 635 GLU ASN SER TYR SER GLY VAL GLU GLY GLU GLY LEU HIS SEQRES 20 A 635 LYS LEU GLY TYR ILE LEU ARG ASP ILE SER LYS ILE PRO SEQRES 21 A 635 GLY GLY ALA MET TYR ALA ASP ASP THR ALA GLY TRP ASP SEQRES 22 A 635 THR ARG ILE THR GLU ASP ASP LEU HIS ASN GLU GLU LYS SEQRES 23 A 635 ILE ILE GLN GLN MET ASP PRO GLU HIS ARG GLN LEU ALA SEQRES 24 A 635 ASN ALA ILE PHE LYS LEU THR TYR GLN ASN LYS VAL VAL SEQRES 25 A 635 LYS VAL GLN ARG PRO THR PRO THR GLY THR VAL MET ASP SEQRES 26 A 635 ILE ILE SER ARG LYS ASP GLN ARG GLY SER GLY GLN VAL SEQRES 27 A 635 GLY THR TYR GLY LEU ASN THR PHE THR ASN MET GLU ALA SEQRES 28 A 635 GLN LEU VAL ARG GLN MET GLU GLY GLU GLY VAL LEU THR SEQRES 29 A 635 LYS ALA ASP LEU GLU ASN PRO HIS LEU LEU GLU LYS LYS SEQRES 30 A 635 ILE THR GLN TRP LEU GLU THR LYS GLY VAL GLU ARG LEU SEQRES 31 A 635 LYS ARG MET ALA ILE SER GLY ASP ASP CYS VAL VAL LYS SEQRES 32 A 635 PRO ILE ASP ASP ARG PHE ALA ASN ALA LEU LEU ALA LEU SEQRES 33 A 635 ASN ASP MET GLY LYS VAL ARG LYS ASP ILE PRO GLN TRP SEQRES 34 A 635 GLN PRO SER LYS GLY TRP HIS ASP TRP GLN GLN VAL PRO SEQRES 35 A 635 PHE CYS SER HIS HIS PHE HIS GLU LEU ILE MET LYS ASP SEQRES 36 A 635 GLY ARG LYS LEU VAL VAL PRO CYS ARG PRO GLN ASP GLU SEQRES 37 A 635 LEU ILE GLY ARG ALA ARG ILE SER GLN GLY ALA GLY TRP SEQRES 38 A 635 SER LEU ARG GLU THR ALA CYS LEU GLY LYS ALA TYR ALA SEQRES 39 A 635 GLN MET TRP SER LEU MET TYR PHE HIS ARG ARG ASP LEU SEQRES 40 A 635 ARG LEU ALA SER ASN ALA ILE CYS SER ALA VAL PRO VAL SEQRES 41 A 635 HIS TRP VAL PRO THR SER ARG THR THR TRP SER ILE HIS SEQRES 42 A 635 ALA HIS HIS GLN TRP MET THR THR GLU ASP MET LEU THR SEQRES 43 A 635 VAL TRP ASN ARG VAL TRP ILE GLU GLU ASN PRO TRP MET SEQRES 44 A 635 GLU ASP LYS THR PRO VAL THR THR TRP GLU ASN VAL PRO SEQRES 45 A 635 TYR LEU GLY LYS ARG GLU ASP GLN TRP CYS GLY SER LEU SEQRES 46 A 635 ILE GLY LEU THR SER ARG ALA THR TRP ALA GLN ASN ILE SEQRES 47 A 635 PRO THR ALA ILE GLN GLN VAL ARG SER LEU ILE GLY ASN SEQRES 48 A 635 GLU GLU PHE LEU ASP TYR MET PRO SER MET LYS ARG PHE SEQRES 49 A 635 ARG LYS GLU GLU GLU SER GLU GLY ALA ILE TRP HET 5V5 A1001 17 HET ZN A1002 1 HET ZN A1003 1 HET PEG A1004 7 HET PEG A1005 7 HET PEG A1006 7 HET PEG A1007 7 HET PEG A1008 7 HET PEG A1009 7 HET PEG A1010 7 HET PEG A1011 4 HETNAM 5V5 2-(4-METHOXY-3-THIOPHEN-2-YL-PHENYL)ETHANOIC ACID HETNAM ZN ZINC ION HETNAM PEG DI(HYDROXYETHYL)ETHER FORMUL 2 5V5 C13 H12 O3 S FORMUL 3 ZN 2(ZN 2+) FORMUL 5 PEG 8(C4 H10 O3) FORMUL 13 HOH *193(H2 O) HELIX 1 AA1 ASN A 272 HIS A 287 1 16 HELIX 2 AA2 ASN A 321 LEU A 327 1 7 HELIX 3 AA3 THR A 328 ASP A 332 5 5 HELIX 4 AA4 VAL A 334 ALA A 341 1 8 HELIX 5 AA5 LEU A 366 GLY A 385 1 20 HELIX 6 AA6 THR A 394 ARG A 403 1 10 HELIX 7 AA7 ALA A 421 GLU A 426 1 6 HELIX 8 AA8 ASP A 427 LEU A 443 1 17 HELIX 9 AA9 ALA A 472 GLY A 489 1 18 HELIX 10 AB1 GLY A 489 ASP A 494 1 6 HELIX 11 AB2 SER A 498 TYR A 503 1 6 HELIX 12 AB3 GLY A 510 LYS A 523 1 14 HELIX 13 AB4 GLY A 536 ILE A 541 5 6 HELIX 14 AB5 THR A 542 GLU A 550 1 9 HELIX 15 AB6 LYS A 551 MET A 556 5 6 HELIX 16 AB7 ASP A 557 TYR A 572 1 16 HELIX 17 AB8 GLY A 604 GLU A 625 1 22 HELIX 18 AB9 THR A 629 ASN A 635 1 7 HELIX 19 AC1 GLU A 640 LYS A 656 1 17 HELIX 20 AC2 ASP A 671 ALA A 677 5 7 HELIX 21 AC3 LEU A 678 MET A 684 1 7 HELIX 22 AC4 ASP A 702 VAL A 706 5 5 HELIX 23 AC5 PRO A 730 ARG A 739 1 10 HELIX 24 AC6 SER A 747 TYR A 766 1 20 HELIX 25 AC7 ARG A 769 VAL A 783 1 15 HELIX 26 AC8 ASP A 808 ILE A 818 1 11 HELIX 27 AC9 THR A 832 VAL A 836 5 5 HELIX 28 AD1 GLY A 840 CYS A 847 1 8 HELIX 29 AD2 LEU A 853 GLY A 875 1 23 SHEET 1 AA1 5 TRP A 291 HIS A 292 0 SHEET 2 AA1 5 ALA A 303 GLU A 309 -1 O SER A 307 N HIS A 292 SHEET 3 AA1 5 VAL A 588 ARG A 594 -1 O MET A 589 N TYR A 308 SHEET 4 AA1 5 LYS A 575 VAL A 579 -1 N VAL A 577 O ILE A 592 SHEET 5 AA1 5 TYR A 451 ASN A 452 1 N TYR A 451 O VAL A 576 SHEET 1 AA2 2 MET A 658 SER A 661 0 SHEET 2 AA2 2 ASP A 664 VAL A 667 -1 O ASP A 664 N SER A 661 SHEET 1 AA3 2 HIS A 712 ILE A 717 0 SHEET 2 AA3 2 LYS A 723 CYS A 728 -1 O LEU A 724 N LEU A 716 LINK OE1 GLU A 437 ZN ZN A1002 1555 1555 2.44 LINK NE2 HIS A 441 ZN ZN A1002 1555 1555 2.08 LINK SG CYS A 446 ZN ZN A1002 1555 1555 2.39 LINK SG CYS A 449 ZN ZN A1002 1555 1555 2.20 LINK NE2 HIS A 712 ZN ZN A1003 1555 1555 2.08 LINK NE2 HIS A 714 ZN ZN A1003 1555 1555 2.15 LINK SG CYS A 728 ZN ZN A1003 1555 1555 2.32 LINK SG CYS A 847 ZN ZN A1003 1555 1555 2.55 SITE 1 AC1 10 LEU A 511 CYS A 709 HIS A 711 ARG A 729 SITE 2 AC1 10 THR A 794 SER A 796 HIS A 798 TRP A 803 SITE 3 AC1 10 HOH A1171 HOH A1191 SITE 1 AC2 4 GLU A 437 HIS A 441 CYS A 446 CYS A 449 SITE 1 AC3 4 HIS A 712 HIS A 714 CYS A 728 CYS A 847 SITE 1 AC4 1 LYS A 630 SITE 1 AC5 4 ASP A 435 ASN A 635 LEU A 639 HOH A1208 SITE 1 AC6 2 PRO A 822 TRP A 823 SITE 1 AC7 4 ARG A 654 ARG A 657 HOH A1106 HOH A1257 SITE 1 AC8 4 SER A 710 HIS A 712 TRP A 846 HOH A1145 SITE 1 AC9 3 TRP A 379 ARG A 382 GLU A 648 SITE 1 AD1 2 VAL A 652 LYS A 656 SITE 1 AD2 2 SER A 747 LEU A 748 CRYST1 164.691 181.210 57.900 90.00 90.00 90.00 C 2 2 21 8 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 0.006072 0.000000 0.000000 0.00000 SCALE2 0.000000 0.005518 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017271 0.00000