HEADER HYDROLASE 09-SEP-14 4WE1 TITLE CRYSTAL STRUCTURE OF HIV-1 REVERSE TRANSCRIPTASE IN COMPLEX WITH 5-(2- TITLE 2 (2-(2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)ETHOXY)PHENOXY)-2- TITLE 3 NAPHTHONITRILE (JLJ600) COMPND MOL_ID: 1; COMPND 2 MOLECULE: GAG-POL POLYPROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 600-1154; COMPND 5 SYNONYM: PR160GAG-POL; COMPND 6 EC: 3.4.23.16,2.7.7.49,2.7.7.7,3.1.26.13,3.1.13.2; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: GAG-POL POLYPROTEIN; COMPND 11 CHAIN: B; COMPND 12 FRAGMENT: UNP RESIDUES 600-1027; COMPND 13 SYNONYM: PR160GAG-POL; COMPND 14 EC: 3.4.23.16,2.7.7.49,2.7.7.7,3.1.26.13,3.1.13.2; COMPND 15 ENGINEERED: YES; COMPND 16 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HUMAN IMMUNODEFICIENCY VIRUS TYPE 1 GROUP M SOURCE 3 SUBTYPE B; SOURCE 4 ORGANISM_COMMON: HIV-1; SOURCE 5 ORGANISM_TAXID: 11678; SOURCE 6 STRAIN: ISOLATE BH10; SOURCE 7 GENE: GAG-POL; SOURCE 8 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 9 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 10 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3); SOURCE 11 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 12 EXPRESSION_SYSTEM_PLASMID: PCDF-2; SOURCE 13 MOL_ID: 2; SOURCE 14 ORGANISM_SCIENTIFIC: HUMAN IMMUNODEFICIENCY VIRUS TYPE 1 GROUP M SOURCE 15 SUBTYPE B; SOURCE 16 ORGANISM_COMMON: HIV-1; SOURCE 17 ORGANISM_TAXID: 11678; SOURCE 18 STRAIN: ISOLATE BH10; SOURCE 19 GENE: GAG-POL; SOURCE 20 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 21 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 22 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3); SOURCE 23 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 24 EXPRESSION_SYSTEM_PLASMID: PCDF-2 KEYWDS POLYMERASE, TRANSFERASE, HYDROLASE, RNASEH, RNASE EXPDTA X-RAY DIFFRACTION AUTHOR K.M.FREY,K.S.ANDERSON REVDAT 4 27-SEP-23 4WE1 1 REMARK REVDAT 3 11-DEC-19 4WE1 1 REMARK REVDAT 2 06-SEP-17 4WE1 1 SOURCE REMARK REVDAT 1 03-DEC-14 4WE1 0 JRNL AUTH W.G.LEE,K.M.FREY,R.GALLARDO-MACIAS,K.A.SPASOV,M.BOLLINI, JRNL AUTH 2 K.S.ANDERSON,W.L.JORGENSEN JRNL TITL PICOMOLAR INHIBITORS OF HIV-1 REVERSE TRANSCRIPTASE: DESIGN JRNL TITL 2 AND CRYSTALLOGRAPHY OF NAPHTHYL PHENYL ETHERS. JRNL REF ACS MED.CHEM.LETT. V. 5 1259 2014 JRNL REFN ISSN 1948-5875 JRNL PMID 25408842 JRNL DOI 10.1021/ML5003713 REMARK 2 REMARK 2 RESOLUTION. 2.49 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 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) : 2.49 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.77 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 3 NUMBER OF REFLECTIONS : 49465 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.240 REMARK 3 R VALUE (WORKING SET) : 0.238 REMARK 3 FREE R VALUE : 0.287 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.040 REMARK 3 FREE R VALUE TEST SET COUNT : 1999 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 38.7696 - 5.9962 0.98 3487 148 0.1976 0.2272 REMARK 3 2 5.9962 - 4.7621 1.00 3482 146 0.2155 0.2443 REMARK 3 3 4.7621 - 4.1610 1.00 3450 145 0.2062 0.2538 REMARK 3 4 4.1610 - 3.7809 1.00 3458 146 0.2292 0.2779 REMARK 3 5 3.7809 - 3.5101 1.00 3411 144 0.2471 0.3209 REMARK 3 6 3.5101 - 3.3032 1.00 3456 146 0.2687 0.3270 REMARK 3 7 3.3032 - 3.1379 1.00 3432 144 0.2789 0.3129 REMARK 3 8 3.1379 - 3.0013 1.00 3432 144 0.2812 0.3405 REMARK 3 9 3.0013 - 2.8858 1.00 3433 145 0.2703 0.3526 REMARK 3 10 2.8858 - 2.7863 1.00 3386 142 0.2688 0.3005 REMARK 3 11 2.7863 - 2.6992 1.00 3410 143 0.2752 0.3355 REMARK 3 12 2.6992 - 2.6220 0.99 3387 143 0.2860 0.3624 REMARK 3 13 2.6220 - 2.5530 0.97 3314 140 0.2903 0.3457 REMARK 3 14 2.5530 - 2.4908 0.86 2928 123 0.3003 0.3793 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) : 0.360 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 32.690 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 50.88 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 60.60 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 7927 REMARK 3 ANGLE : 0.858 10783 REMARK 3 CHIRALITY : 0.033 1170 REMARK 3 PLANARITY : 0.004 1353 REMARK 3 DIHEDRAL : 14.418 2971 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 4WE1 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-SEP-14. REMARK 100 THE DEPOSITION ID IS D_1000202746. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-OCT-13 REMARK 200 TEMPERATURE (KELVIN) : 80 REMARK 200 PH : 6.0-6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X29A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.075 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 49497 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.490 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 (%) : 98.9 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06500 REMARK 200 FOR THE DATA SET : 15.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.49 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.53 REMARK 200 COMPLETENESS FOR SHELL (%) : 89.7 REMARK 200 DATA REDUNDANCY IN SHELL : 3.10 REMARK 200 R MERGE FOR SHELL (I) : 0.37300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.970 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: PDB CODE:4MFB REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 61.11 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.16 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 18% W/V PEG 8000, 100 MM AMMONIUM REMARK 280 SULFATE, 15 MM MAGNESIUM SULFATE, 50 MM IMIDAZOLE (PH 6.5), AND REMARK 280 5 MM SPERMINE-HCL, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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 110.13550 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 33.60900 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 110.13550 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 33.60900 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: 5920 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 45620 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -91.0 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 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 MET A -1 REMARK 465 VAL A 0 REMARK 465 PRO A 1 REMARK 465 ASP A 67 REMARK 465 SER A 68 REMARK 465 GLU A 138 REMARK 465 THR A 139 REMARK 465 PRO A 140 REMARK 465 ASP A 549 REMARK 465 LYS A 550 REMARK 465 LEU A 551 REMARK 465 VAL A 552 REMARK 465 SER A 553 REMARK 465 ALA A 554 REMARK 465 GLY A 555 REMARK 465 PRO B 1 REMARK 465 ILE B 2 REMARK 465 SER B 3 REMARK 465 LYS B 66 REMARK 465 ASP B 67 REMARK 465 TRP B 88 REMARK 465 GLU B 89 REMARK 465 VAL B 90 REMARK 465 GLN B 91 REMARK 465 LEU B 92 REMARK 465 GLY B 93 REMARK 465 ILE B 94 REMARK 465 ASP B 218 REMARK 465 LYS B 219 REMARK 465 LYS B 220 REMARK 465 HIS B 221 REMARK 465 GLN B 222 REMARK 465 LYS B 223 REMARK 465 GLU B 224 REMARK 465 PRO B 225 REMARK 465 PRO B 226 REMARK 465 PHE B 227 REMARK 465 LEU B 228 REMARK 465 TRP B 229 REMARK 465 MET B 230 REMARK 465 GLY B 231 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 ILE A 2 CG1 CG2 CD1 REMARK 470 LEU A 26 CG CD1 CD2 REMARK 470 THR A 27 OG1 CG2 REMARK 470 GLU A 28 CG CD OE1 OE2 REMARK 470 LYS A 64 CG CD CE NZ REMARK 470 LYS A 65 CG CD CE NZ REMARK 470 LYS A 66 CG CD CE NZ REMARK 470 LYS A 70 CG CD CE NZ REMARK 470 ASN A 137 CG OD1 ND2 REMARK 470 LYS A 220 CG CD CE NZ REMARK 470 LYS A 287 CG CD CE NZ REMARK 470 GLU B 6 CG CD OE1 OE2 REMARK 470 LYS B 65 CG CD CE NZ REMARK 470 LYS B 70 CG CD CE NZ REMARK 470 ASP B 86 CG OD1 OD2 REMARK 470 PHE B 87 CG CD1 CD2 CE1 CE2 CZ REMARK 470 ARG B 358 CG CD NE CZ NH1 NH2 REMARK 470 THR B 419 OG1 CG2 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 LEU A 92 -64.61 -103.77 REMARK 500 MET A 184 -123.38 51.35 REMARK 500 ILE A 270 -58.61 -128.16 REMARK 500 THR A 290 -60.70 -144.91 REMARK 500 LYS A 451 -4.92 67.19 REMARK 500 ASN A 545 -143.27 52.11 REMARK 500 MET B 184 -120.42 56.92 REMARK 500 PHE B 346 -4.16 70.91 REMARK 500 ALA B 360 -7.73 66.41 REMARK 500 ASN B 418 -65.54 -97.84 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 ASN A 54 PRO A 55 -33.99 REMARK 500 PRO B 420 PRO B 421 -143.71 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 MG A 602 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 185 OD1 REMARK 620 2 ASP A 186 OD1 83.3 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 603 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 443 OD1 REMARK 620 2 GLU A 478 OE2 68.0 REMARK 620 3 ASP A 498 OD1 105.3 81.0 REMARK 620 4 ASP A 498 OD2 95.0 123.2 50.6 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 3LQ A 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 603 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 604 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 605 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 606 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 607 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4H4M RELATED DB: PDB REMARK 900 RELATED ID: 4H4O RELATED DB: PDB REMARK 900 RELATED ID: 4MFB RELATED DB: PDB DBREF 4WE1 A 1 555 UNP P03366 POL_HV1B1 600 1154 DBREF 4WE1 B 1 428 UNP P03366 POL_HV1B1 600 1027 SEQADV 4WE1 MET A -1 UNP P03366 INITIATING METHIONINE SEQADV 4WE1 VAL A 0 UNP P03366 EXPRESSION TAG SEQADV 4WE1 ALA A 172 UNP P03366 LYS 771 ENGINEERED MUTATION SEQADV 4WE1 ALA A 173 UNP P03366 LYS 772 ENGINEERED MUTATION SEQADV 4WE1 SER A 280 UNP P03366 CYS 879 ENGINEERED MUTATION SEQADV 4WE1 SER B 280 UNP P03366 CYS 879 ENGINEERED MUTATION SEQRES 1 A 557 MET VAL PRO ILE SER PRO ILE GLU THR VAL PRO VAL LYS SEQRES 2 A 557 LEU LYS PRO GLY MET ASP GLY PRO LYS VAL LYS GLN TRP SEQRES 3 A 557 PRO LEU THR GLU GLU LYS ILE LYS ALA LEU VAL GLU ILE SEQRES 4 A 557 CYS THR GLU MET GLU LYS GLU GLY LYS ILE SER LYS ILE SEQRES 5 A 557 GLY PRO GLU ASN PRO TYR ASN THR PRO VAL PHE ALA ILE SEQRES 6 A 557 LYS LYS LYS ASP SER THR LYS TRP ARG LYS LEU VAL ASP SEQRES 7 A 557 PHE ARG GLU LEU ASN LYS ARG THR GLN ASP PHE TRP GLU SEQRES 8 A 557 VAL GLN LEU GLY ILE PRO HIS PRO ALA GLY LEU LYS LYS SEQRES 9 A 557 LYS LYS SER VAL THR VAL LEU ASP VAL GLY ASP ALA TYR SEQRES 10 A 557 PHE SER VAL PRO LEU ASP GLU ASP PHE ARG LYS TYR THR SEQRES 11 A 557 ALA PHE THR ILE PRO SER ILE ASN ASN GLU THR PRO GLY SEQRES 12 A 557 ILE ARG TYR GLN TYR ASN VAL LEU PRO GLN GLY TRP LYS SEQRES 13 A 557 GLY SER PRO ALA ILE PHE GLN SER SER MET THR LYS ILE SEQRES 14 A 557 LEU GLU PRO PHE ALA ALA GLN ASN PRO ASP ILE VAL ILE SEQRES 15 A 557 TYR GLN TYR MET ASP ASP LEU TYR VAL GLY SER ASP LEU SEQRES 16 A 557 GLU ILE GLY GLN HIS ARG THR LYS ILE GLU GLU LEU ARG SEQRES 17 A 557 GLN HIS LEU LEU ARG TRP GLY LEU THR THR PRO ASP LYS SEQRES 18 A 557 LYS HIS GLN LYS GLU PRO PRO PHE LEU TRP MET GLY TYR SEQRES 19 A 557 GLU LEU HIS PRO ASP LYS TRP THR VAL GLN PRO ILE VAL SEQRES 20 A 557 LEU PRO GLU LYS ASP SER TRP THR VAL ASN ASP ILE GLN SEQRES 21 A 557 LYS LEU VAL GLY LYS LEU ASN TRP ALA SER GLN ILE TYR SEQRES 22 A 557 PRO GLY ILE LYS VAL ARG GLN LEU SER LYS LEU LEU ARG SEQRES 23 A 557 GLY THR LYS ALA LEU THR GLU VAL ILE PRO LEU THR GLU SEQRES 24 A 557 GLU ALA GLU LEU GLU LEU ALA GLU ASN ARG GLU ILE LEU SEQRES 25 A 557 LYS GLU PRO VAL HIS GLY VAL TYR TYR ASP PRO SER LYS SEQRES 26 A 557 ASP LEU ILE ALA GLU ILE GLN LYS GLN GLY GLN GLY GLN SEQRES 27 A 557 TRP THR TYR GLN ILE TYR GLN GLU PRO PHE LYS ASN LEU SEQRES 28 A 557 LYS THR GLY LYS TYR ALA ARG MET ARG GLY ALA HIS THR SEQRES 29 A 557 ASN ASP VAL LYS GLN LEU THR GLU ALA VAL GLN LYS ILE SEQRES 30 A 557 THR THR GLU SER ILE VAL ILE TRP GLY LYS THR PRO LYS SEQRES 31 A 557 PHE LYS LEU PRO ILE GLN LYS GLU THR TRP GLU THR TRP SEQRES 32 A 557 TRP THR GLU TYR TRP GLN ALA THR TRP ILE PRO GLU TRP SEQRES 33 A 557 GLU PHE VAL ASN THR PRO PRO LEU VAL LYS LEU TRP TYR SEQRES 34 A 557 GLN LEU GLU LYS GLU PRO ILE VAL GLY ALA GLU THR PHE SEQRES 35 A 557 TYR VAL ASP GLY ALA ALA ASN ARG GLU THR LYS LEU GLY SEQRES 36 A 557 LYS ALA GLY TYR VAL THR ASN LYS GLY ARG GLN LYS VAL SEQRES 37 A 557 VAL PRO LEU THR ASN THR THR ASN GLN LYS THR GLU LEU SEQRES 38 A 557 GLN ALA ILE TYR LEU ALA LEU GLN ASP SER GLY LEU GLU SEQRES 39 A 557 VAL ASN ILE VAL THR ASP SER GLN TYR ALA LEU GLY ILE SEQRES 40 A 557 ILE GLN ALA GLN PRO ASP LYS SER GLU SER GLU LEU VAL SEQRES 41 A 557 ASN GLN ILE ILE GLU GLN LEU ILE LYS LYS GLU LYS VAL SEQRES 42 A 557 TYR LEU ALA TRP VAL PRO ALA HIS LYS GLY ILE GLY GLY SEQRES 43 A 557 ASN GLU GLN VAL ASP LYS LEU VAL SER ALA GLY SEQRES 1 B 428 PRO ILE SER PRO ILE GLU THR VAL PRO VAL LYS LEU LYS SEQRES 2 B 428 PRO GLY MET ASP GLY PRO LYS VAL LYS GLN TRP PRO LEU SEQRES 3 B 428 THR GLU GLU LYS ILE LYS ALA LEU VAL GLU ILE CYS THR SEQRES 4 B 428 GLU MET GLU LYS GLU GLY LYS ILE SER LYS ILE GLY PRO SEQRES 5 B 428 GLU ASN PRO TYR ASN THR PRO VAL PHE ALA ILE LYS LYS SEQRES 6 B 428 LYS ASP SER THR LYS TRP ARG LYS LEU VAL ASP PHE ARG SEQRES 7 B 428 GLU LEU ASN LYS ARG THR GLN ASP PHE TRP GLU VAL GLN SEQRES 8 B 428 LEU GLY ILE PRO HIS PRO ALA GLY LEU LYS LYS LYS LYS SEQRES 9 B 428 SER VAL THR VAL LEU ASP VAL GLY ASP ALA TYR PHE SER SEQRES 10 B 428 VAL PRO LEU ASP GLU ASP PHE ARG LYS TYR THR ALA PHE SEQRES 11 B 428 THR ILE PRO SER ILE ASN ASN GLU THR PRO GLY ILE ARG SEQRES 12 B 428 TYR GLN TYR ASN VAL LEU PRO GLN GLY TRP LYS GLY SER SEQRES 13 B 428 PRO ALA ILE PHE GLN SER SER MET THR LYS ILE LEU GLU SEQRES 14 B 428 PRO PHE LYS LYS GLN ASN PRO ASP ILE VAL ILE TYR GLN SEQRES 15 B 428 TYR MET ASP ASP LEU TYR VAL GLY SER ASP LEU GLU ILE SEQRES 16 B 428 GLY GLN HIS ARG THR LYS ILE GLU GLU LEU ARG GLN HIS SEQRES 17 B 428 LEU LEU ARG TRP GLY LEU THR THR PRO ASP LYS LYS HIS SEQRES 18 B 428 GLN LYS GLU PRO PRO PHE LEU TRP MET GLY TYR GLU LEU SEQRES 19 B 428 HIS PRO ASP LYS TRP THR VAL GLN PRO ILE VAL LEU PRO SEQRES 20 B 428 GLU LYS ASP SER TRP THR VAL ASN ASP ILE GLN LYS LEU SEQRES 21 B 428 VAL GLY LYS LEU ASN TRP ALA SER GLN ILE TYR PRO GLY SEQRES 22 B 428 ILE LYS VAL ARG GLN LEU SER LYS LEU LEU ARG GLY THR SEQRES 23 B 428 LYS ALA LEU THR GLU VAL ILE PRO LEU THR GLU GLU ALA SEQRES 24 B 428 GLU LEU GLU LEU ALA GLU ASN ARG GLU ILE LEU LYS GLU SEQRES 25 B 428 PRO VAL HIS GLY VAL TYR TYR ASP PRO SER LYS ASP LEU SEQRES 26 B 428 ILE ALA GLU ILE GLN LYS GLN GLY GLN GLY GLN TRP THR SEQRES 27 B 428 TYR GLN ILE TYR GLN GLU PRO PHE LYS ASN LEU LYS THR SEQRES 28 B 428 GLY LYS TYR ALA ARG MET ARG GLY ALA HIS THR ASN ASP SEQRES 29 B 428 VAL LYS GLN LEU THR GLU ALA VAL GLN LYS ILE THR THR SEQRES 30 B 428 GLU SER ILE VAL ILE TRP GLY LYS THR PRO LYS PHE LYS SEQRES 31 B 428 LEU PRO ILE GLN LYS GLU THR TRP GLU THR TRP TRP THR SEQRES 32 B 428 GLU TYR TRP GLN ALA THR TRP ILE PRO GLU TRP GLU PHE SEQRES 33 B 428 VAL ASN THR PRO PRO LEU VAL LYS LEU TRP TYR GLN HET 3LQ A 601 30 HET MG A 602 1 HET MG A 603 1 HET SO4 A 604 5 HET SO4 A 605 5 HET SO4 A 606 5 HET SO4 A 607 5 HETNAM 3LQ 5-{2-[2-(2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL) HETNAM 2 3LQ ETHOXY]PHENOXY}NAPHTHALENE-2-CARBONITRILE HETNAM MG MAGNESIUM ION HETNAM SO4 SULFATE ION FORMUL 3 3LQ C23 H17 N3 O4 FORMUL 4 MG 2(MG 2+) FORMUL 6 SO4 4(O4 S 2-) FORMUL 10 HOH *84(H2 O) HELIX 1 AA1 GLU A 29 GLU A 44 1 16 HELIX 2 AA2 PHE A 77 THR A 84 1 8 HELIX 3 AA3 HIS A 96 LEU A 100 5 5 HELIX 4 AA4 ALA A 114 VAL A 118 5 5 HELIX 5 AA5 ASP A 121 ALA A 129 5 9 HELIX 6 AA6 GLY A 155 GLN A 174 1 20 HELIX 7 AA7 GLU A 194 TRP A 212 1 19 HELIX 8 AA8 THR A 253 GLN A 269 1 17 HELIX 9 AA9 VAL A 276 LEU A 283 1 8 HELIX 10 AB1 THR A 296 LEU A 310 1 15 HELIX 11 AB2 ASN A 363 GLY A 384 1 22 HELIX 12 AB3 GLN A 394 TYR A 405 1 12 HELIX 13 AB4 THR A 473 SER A 489 1 17 HELIX 14 AB5 SER A 499 ALA A 508 1 10 HELIX 15 AB6 SER A 515 LYS A 528 1 14 HELIX 16 AB7 THR B 27 GLU B 44 1 18 HELIX 17 AB8 PHE B 77 THR B 84 1 8 HELIX 18 AB9 GLY B 99 LYS B 103 5 5 HELIX 19 AC1 GLY B 112 VAL B 118 5 7 HELIX 20 AC2 ASP B 121 LYS B 126 1 6 HELIX 21 AC3 TYR B 127 ALA B 129 5 3 HELIX 22 AC4 SER B 134 GLU B 138 5 5 HELIX 23 AC5 LYS B 154 PHE B 160 1 7 HELIX 24 AC6 PHE B 160 ASN B 175 1 16 HELIX 25 AC7 GLU B 194 TRP B 212 1 19 HELIX 26 AC8 HIS B 235 TRP B 239 5 5 HELIX 27 AC9 THR B 253 GLN B 269 1 17 HELIX 28 AD1 VAL B 276 LEU B 282 1 7 HELIX 29 AD2 THR B 296 LEU B 310 1 15 HELIX 30 AD3 ASN B 363 GLY B 384 1 22 HELIX 31 AD4 GLN B 394 TRP B 406 1 13 HELIX 32 AD5 LEU B 422 GLN B 428 1 7 SHEET 1 AA1 3 ILE A 47 LYS A 49 0 SHEET 2 AA1 3 ILE A 142 TYR A 146 -1 O GLN A 145 N SER A 48 SHEET 3 AA1 3 PHE A 130 ILE A 132 -1 N PHE A 130 O TYR A 144 SHEET 1 AA2 2 VAL A 60 ILE A 63 0 SHEET 2 AA2 2 ARG A 72 VAL A 75 -1 O ARG A 72 N ILE A 63 SHEET 1 AA3 3 SER A 105 LEU A 109 0 SHEET 2 AA3 3 ASP A 186 SER A 191 -1 O LEU A 187 N LEU A 109 SHEET 3 AA3 3 VAL A 179 TYR A 183 -1 N TYR A 181 O TYR A 188 SHEET 1 AA4 3 PHE A 227 TRP A 229 0 SHEET 2 AA4 3 TYR A 232 LEU A 234 -1 O LEU A 234 N PHE A 227 SHEET 3 AA4 3 TRP A 239 VAL A 241 -1 O THR A 240 N GLU A 233 SHEET 1 AA5 5 ASN A 348 TYR A 354 0 SHEET 2 AA5 5 TRP A 337 TYR A 342 -1 N ILE A 341 O LYS A 350 SHEET 3 AA5 5 ILE A 326 LYS A 331 -1 N GLN A 330 O THR A 338 SHEET 4 AA5 5 LYS A 388 LEU A 391 1 O LYS A 388 N ALA A 327 SHEET 5 AA5 5 TRP A 414 PHE A 416 1 O GLU A 415 N PHE A 389 SHEET 1 AA6 2 HIS A 361 THR A 362 0 SHEET 2 AA6 2 LYS A 512 SER A 513 -1 O LYS A 512 N THR A 362 SHEET 1 AA7 5 GLN A 464 LEU A 469 0 SHEET 2 AA7 5 GLY A 453 THR A 459 -1 N ALA A 455 O VAL A 467 SHEET 3 AA7 5 GLU A 438 ALA A 446 -1 N ASP A 443 O GLY A 456 SHEET 4 AA7 5 GLU A 492 THR A 497 1 O ASN A 494 N PHE A 440 SHEET 5 AA7 5 LYS A 530 TRP A 535 1 O TYR A 532 N ILE A 495 SHEET 1 AA8 3 ILE B 47 LYS B 49 0 SHEET 2 AA8 3 ILE B 142 TYR B 146 -1 O GLN B 145 N SER B 48 SHEET 3 AA8 3 PHE B 130 ILE B 132 -1 N ILE B 132 O ILE B 142 SHEET 1 AA9 2 VAL B 60 ILE B 63 0 SHEET 2 AA9 2 ARG B 72 VAL B 75 -1 O ARG B 72 N ILE B 63 SHEET 1 AB1 4 VAL B 179 TYR B 183 0 SHEET 2 AB1 4 ASP B 186 SER B 191 -1 O TYR B 188 N TYR B 181 SHEET 3 AB1 4 SER B 105 ASP B 110 -1 N SER B 105 O SER B 191 SHEET 4 AB1 4 GLU B 233 LEU B 234 -1 O LEU B 234 N VAL B 106 SHEET 1 AB2 5 ASN B 348 ALA B 355 0 SHEET 2 AB2 5 GLN B 336 TYR B 342 -1 N ILE B 341 O LYS B 350 SHEET 3 AB2 5 ILE B 326 GLY B 333 -1 N ILE B 326 O TYR B 342 SHEET 4 AB2 5 LYS B 388 LEU B 391 1 O LYS B 390 N ALA B 327 SHEET 5 AB2 5 TRP B 414 PHE B 416 1 O GLU B 415 N LEU B 391 LINK OD1 ASP A 185 MG MG A 602 1555 1555 2.46 LINK OD1 ASP A 186 MG MG A 602 1555 1555 2.51 LINK OD1 ASP A 443 MG MG A 603 1555 1555 2.98 LINK OE2 GLU A 478 MG MG A 603 1555 1555 2.37 LINK OD1 ASP A 498 MG MG A 603 1555 1555 2.22 LINK OD2 ASP A 498 MG MG A 603 1555 1555 2.76 CISPEP 1 PRO A 25 LEU A 26 0 -5.59 CISPEP 2 PRO A 225 PRO A 226 0 -0.71 CISPEP 3 PRO A 420 PRO A 421 0 0.17 SITE 1 AC1 16 LEU A 100 LYS A 101 LYS A 102 LYS A 103 SITE 2 AC1 16 VAL A 106 VAL A 108 VAL A 179 TYR A 181 SITE 3 AC1 16 TYR A 188 GLY A 190 PHE A 227 TRP A 229 SITE 4 AC1 16 LEU A 234 HIS A 235 PRO A 236 TYR A 318 SITE 1 AC2 3 ASP A 110 ASP A 185 ASP A 186 SITE 1 AC3 3 ASP A 443 GLU A 478 ASP A 498 SITE 1 AC4 3 ARG A 448 THR A 473 ASN A 474 SITE 1 AC5 5 LYS A 476 SER A 515 GLU A 516 LEU A 517 SITE 2 AC5 5 HOH A 729 SITE 1 AC6 4 ARG A 277 ARG A 356 MET A 357 ARG A 358 SITE 1 AC7 5 LYS A 353 TYR A 354 ALA A 355 ARG A 356 SITE 2 AC7 5 LYS A 374 CRYST1 220.271 67.218 102.483 90.00 108.08 90.00 C 1 2 1 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 0.004540 0.000000 0.001482 0.00000 SCALE2 0.000000 0.014877 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010265 0.00000