HEADER HYDROLASE/HYDROLASE INHIBITOR 26-FEB-13 4JE2 OBSLTE 04-JUN-14 4JE2 4QAG TITLE STRUCTURE OF A DIHYDROXYCOUMARIN ACTIVE-SITE INHIBITOR IN COMPLEX WITH TITLE 2 THE RNASE H DOMAIN OF HIV-1 REVERSE TRANSCRIPTASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNASE H; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: EXORIBONUCLEASE H; COMPND 5 EC: 3.1.13.2; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HUMAN IMMUNODEFICIENCY VIRUS TYPE 1; SOURCE 3 ORGANISM_COMMON: HIV-1; SOURCE 4 ORGANISM_TAXID: 11678; SOURCE 5 GENE: GAG-POL; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PLYSS KEYWDS RNASE H INHIBITOR, STRUCTURE-BASED DRUG DESIGN, ACTIVE SITE, KEYWDS 2 DIHYDROXYCOUMARIN ANALOGS, DIHYDROXY-BENZOPYRONE DERIVATIVES, KEYWDS 3 DIVALENT CATION CHELATOR, AIDS, REVERSE TRANSCRIPTASE, PROTEIN- KEYWDS 4 INHIBITOR COMPLEX, HYDROLASE-HYDROLASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR D.M.HIMMEL,W.C.HO,E.ARNOLD REVDAT 3 04-JUN-14 4JE2 1 OBSLTE REVDAT 2 19-MAR-14 4JE2 1 JRNL REVDAT 1 05-MAR-14 4JE2 0 JRNL AUTH D.M.HIMMEL,N.S.MYSHAKINA,T.ILINA,A.VAN RY,W.C.HO, JRNL AUTH 2 M.A.PARNIAK,E.ARNOLD JRNL TITL STRUCTURE OF A DIHYDROXYCOUMARIN ACTIVE-SITE INHIBITOR IN JRNL TITL 2 COMPLEX WITH THE RNASE H DOMAIN OF HIV-1 REVERSE JRNL TITL 3 TRANSCRIPTASE AND STRUCTURE-ACTIVITY ANALYSIS OF INHIBITOR JRNL TITL 4 ANALOGS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH D.M.HIMMEL,K.A.MAEGLEY,T.A.PAULY,J.D.BAUMAN,K.DAS,C.DHARIA, REMARK 1 AUTH 2 A.D.CLARK JR.,K.RYAN,M.J.HICKEY,R.A.LOVE,S.H.HUGHES, REMARK 1 AUTH 3 S.BERGQVIST,E.ARNOLD REMARK 1 TITL STRUCTURE OF HIV-1 REVERSE TRANSCRIPTASE WITH THE INHIBITOR REMARK 1 TITL 2 BETA-THUJAPLICINOL BOUND AT THE RNASE H ACTIVE SITE REMARK 1 REF STRUCTURE V. 17 1625 2009 REMARK 1 REFN ISSN 0969-2126 REMARK 1 REFERENCE 2 REMARK 1 AUTH S.CHUNG,D.M.HIMMEL,J.JIANG,K.WOJTAK,J.D.BAUMAN,J.W.RAUSCH, REMARK 1 AUTH 2 J.A.WILSON,J.A.BEUTLER,C.J.THOMAS,E.ARNOLD,S.F.J.LE GRICE REMARK 1 TITL SYNTHESIS, ACTIVITY, AND STRUCTURAL ANALYSIS OF NOVEL REMARK 1 TITL 2 ALPHA-HYDROXYTROPOLONE INHIBITORS OF HUMAN IMMUNODEFICIENCY REMARK 1 TITL 3 VIRUS REVERSE TRANSCRIPTASE-ASSOCIATED RIBONUCLEASE H REMARK 1 REF J.MED.CHEM. V. 54 4462 2011 REMARK 1 REFN ISSN 0022-2623 REMARK 1 REFERENCE 3 REMARK 1 AUTH K.DAS,J.D.BAUMAN,A.D.CLARK JR.,Y.V.FRENKEL,P.J.LEWI, REMARK 1 AUTH 2 A.J.SHATKIN,S.H.HUGHES,E.ARNOLD REMARK 1 TITL HIGH-RESOLUTION STRUCTURES OF HIV-1 REVERSE REMARK 1 TITL 2 TRANSCRIPTASE/TMC278 COMPLEXES: STRATEGIC FLEXIBILITY REMARK 1 TITL 3 EXPLAINS POTENCY AGAINST RESISTANCE MUTATIONS REMARK 1 REF PROC.NATL.ACAD.SCI.USA V. 105 1466 2008 REMARK 1 REFN ISSN 0027-8424 REMARK 1 REFERENCE 4 REMARK 1 AUTH D.M.HIMMEL,S.G.SARAFIANOS,S.DHARMASENA,M.M.HOSSAIN, REMARK 1 AUTH 2 K.MCCOY-SIMANDLE,T.ILINA,A.D.CLARK JR.,J.L.KNIGHT, REMARK 1 AUTH 3 J.G.JULIAS,P.K.CLARK,K.KROGH-JESPERSEN,R.M.LEVY,S.H.HUGHES, REMARK 1 AUTH 4 M.A.PARNIAK,E.ARNOLD REMARK 1 TITL HIV-1 REVERSE TRANSCRIPTASE STRUCTURE WITH RNASE H INHIBITOR REMARK 1 TITL 2 DIHYDROXY BENZOYL NAPHTHYL HYDRAZONE BOUND AT A NOVEL SITE REMARK 1 REF ACS CHEM.BIOL. V. 1 702 2006 REMARK 1 REFN ISSN 1554-8929 REMARK 2 REMARK 2 RESOLUTION. 1.65 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8_1066) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE- REMARK 3 : KUNSTLEVE,LI-WEI HUNG,ROBERT IMMORMINO, REMARK 3 : TOM IOERGER,AIRLIE MCCOY,ERIK MCKEE,NIGEL REMARK 3 : MORIARTY,REETAL PAI,RANDY READ,JANE REMARK 3 : RICHARDSON,DAVID RICHARDSON,TOD ROMO,JIM REMARK 3 : SACCHETTINI,NICHOLAS SAUTER,JACOB SMITH, REMARK 3 : LAURENT STORONI,TOM TERWILLIGER,PETER REMARK 3 : ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.65 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.76 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.010 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.2 REMARK 3 NUMBER OF REFLECTIONS : 36905 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.185 REMARK 3 R VALUE (WORKING SET) : 0.185 REMARK 3 FREE R VALUE : 0.195 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 2.740 REMARK 3 FREE R VALUE TEST SET COUNT : 1013 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 34.7590 - 3.1628 1.00 5421 163 0.1669 0.1753 REMARK 3 2 3.1628 - 2.5106 1.00 5458 137 0.1961 0.1939 REMARK 3 3 2.5106 - 2.1933 0.99 5433 142 0.1776 0.2171 REMARK 3 4 2.1933 - 1.9928 0.99 5432 151 0.1727 0.1784 REMARK 3 5 1.9928 - 1.8500 0.98 5344 162 0.2065 0.2205 REMARK 3 6 1.8500 - 1.7409 0.95 5156 155 0.3019 0.3403 REMARK 3 7 1.7409 - 1.6540 0.68 3648 103 0.3991 0.4160 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) : 0.230 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.320 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 31.66 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 56.69 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 : 0.009 2158 REMARK 3 ANGLE : 0.918 2930 REMARK 3 CHIRALITY : 0.052 330 REMARK 3 PLANARITY : 0.003 372 REMARK 3 DIHEDRAL : 15.310 798 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 4JE2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-MAR-13. REMARK 100 THE RCSB ID CODE IS RCSB077928. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-JUN-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X25 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.10 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 37907 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.650 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.7 REMARK 200 DATA REDUNDANCY : 9.100 REMARK 200 R MERGE (I) : 0.08200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 21.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.65 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.71 REMARK 200 COMPLETENESS FOR SHELL (%) : 70.3 REMARK 200 DATA REDUNDANCY IN SHELL : 2.60 REMARK 200 R MERGE FOR SHELL (I) : 0.74000 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: PDB ENTRY 3IG1 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.26 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.88 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM BICINE PH 8.2, 10 MM MANGANESE REMARK 280 SULFATE, 1 MM SODIUM AZIDE, 9% PEG 3350, COMBINED WITH EQUAL REMARK 280 VOLUME OF 10 MM TRIS PH 8.0, 75 MM NACL, 20 MG/ML (1.34 MM) RNASE REMARK 280 H. INHIBITOR WAS SOAKED INTO THE CRYSTAL, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 318K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 37.36567 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 74.73133 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3 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 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 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 350 REMARK 350 BIOMOLECULE: 3 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1700 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13880 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -21.0 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 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 TRP A 426 TYR A 427 104.28 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A1002 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 F95 A1001 O1 REMARK 620 2 ASP A 549 OD1 161.8 REMARK 620 3 HOH A1112 O 87.7 91.9 REMARK 620 4 ASP A 443 OD1 100.7 97.5 89.9 REMARK 620 5 HOH A1113 O 89.3 91.2 176.9 90.1 REMARK 620 6 F95 A1001 O2 80.1 81.8 92.8 177.2 87.2 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN B 603 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 F95 B 601 O1 REMARK 620 2 ASP B 443 OD2 93.8 REMARK 620 3 ASP B 498 OD1 135.5 121.6 REMARK 620 4 GLU B 478 OE1 110.3 87.8 98.1 REMARK 620 5 ASP B 498 OD2 98.2 92.6 57.8 151.5 REMARK 620 6 F95 B 601 O3 73.1 158.9 78.2 81.5 105.4 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A1003 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 478 OE2 REMARK 620 2 ASP A 443 OD2 94.5 REMARK 620 3 ASP A 498 OD1 104.2 116.8 REMARK 620 4 F95 A1001 O1 116.0 89.5 129.9 REMARK 620 5 ASP A 498 OD2 156.5 84.8 56.4 87.5 REMARK 620 6 F95 A1001 O3 85.7 162.1 80.4 74.5 102.1 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN B 602 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 549 OD1 REMARK 620 2 F95 B 601 O1 162.5 REMARK 620 3 ASP B 443 OD1 99.1 98.4 REMARK 620 4 HOH B 717 O 89.1 91.9 93.1 REMARK 620 5 HOH B 705 O 89.9 89.5 85.6 178.2 REMARK 620 6 F95 B 601 O2 82.4 80.2 178.1 88.1 93.3 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 F95 A 1001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 1002 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 1003 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE F95 B 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN B 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN B 603 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3K2P RELATED DB: PDB REMARK 900 HIV-1 RNASE H DOMAIN IN COMPLEX WITH BETA-THUJAPLICINOL, AN REMARK 900 ACTIVE SITE RNASE H INHIBITOR REMARK 900 RELATED ID: 3IG1 RELATED DB: PDB REMARK 900 FULL-LENGTH HIV-1 REVERSE TRANSCRIPTASE IN COMPLEX WITH REMARK 900 BETA-THUJAPLICINOL, AN ACTIVE SITE RNASE H INHIBITOR REMARK 900 RELATED ID: 3QLH RELATED DB: PDB REMARK 900 FULL-LENGTH HIV-1 REVERSE TRANSCRIPTASE IN COMPLEX WITH REMARK 900 TMC278 (RILPIVIRINE) AND MANICOL REMARK 900 RELATED ID: 3IFJ RELATED DB: PDB REMARK 900 FULL-LENGTH HIV-1 REVERSE TRANSCRIPTASE IN COMPLEX WITH REMARK 900 DHBNH, AN ALLOSTERIC RNASE H INHIBITOR REMARK 900 RELATED ID: 2ZD1 RELATED DB: PDB REMARK 900 FULL-LENGTH HIV-1 REVERSE TRANSCRIPTASE IN COMPLEX WITH REMARK 900 TMC278 (RILPIVIRINE) DBREF 4JE2 A 425 557 UNP P03366 POL_HV1B1 1024 1156 DBREF 4JE2 B 425 557 UNP P03366 POL_HV1B1 1024 1156 SEQRES 1 A 133 LEU TRP TYR GLN LEU GLU LYS GLU PRO ILE VAL GLY ALA SEQRES 2 A 133 GLU THR PHE TYR VAL ASP GLY ALA ALA ASN ARG GLU THR SEQRES 3 A 133 LYS LEU GLY LYS ALA GLY TYR VAL THR ASN LYS GLY ARG SEQRES 4 A 133 GLN LYS VAL VAL PRO LEU THR ASN THR THR ASN GLN LYS SEQRES 5 A 133 THR GLU LEU GLN ALA ILE TYR LEU ALA LEU GLN ASP SER SEQRES 6 A 133 GLY LEU GLU VAL ASN ILE VAL THR ASP SER GLN TYR ALA SEQRES 7 A 133 LEU GLY ILE ILE GLN ALA GLN PRO ASP LYS SER GLU SER SEQRES 8 A 133 GLU LEU VAL ASN GLN ILE ILE GLU GLN LEU ILE LYS LYS SEQRES 9 A 133 GLU LYS VAL TYR LEU ALA TRP VAL PRO ALA HIS LYS GLY SEQRES 10 A 133 ILE GLY GLY ASN GLU GLN VAL ASP LYS LEU VAL SER ALA SEQRES 11 A 133 GLY ILE ARG SEQRES 1 B 133 LEU TRP TYR GLN LEU GLU LYS GLU PRO ILE VAL GLY ALA SEQRES 2 B 133 GLU THR PHE TYR VAL ASP GLY ALA ALA ASN ARG GLU THR SEQRES 3 B 133 LYS LEU GLY LYS ALA GLY TYR VAL THR ASN LYS GLY ARG SEQRES 4 B 133 GLN LYS VAL VAL PRO LEU THR ASN THR THR ASN GLN LYS SEQRES 5 B 133 THR GLU LEU GLN ALA ILE TYR LEU ALA LEU GLN ASP SER SEQRES 6 B 133 GLY LEU GLU VAL ASN ILE VAL THR ASP SER GLN TYR ALA SEQRES 7 B 133 LEU GLY ILE ILE GLN ALA GLN PRO ASP LYS SER GLU SER SEQRES 8 B 133 GLU LEU VAL ASN GLN ILE ILE GLU GLN LEU ILE LYS LYS SEQRES 9 B 133 GLU LYS VAL TYR LEU ALA TRP VAL PRO ALA HIS LYS GLY SEQRES 10 B 133 ILE GLY GLY ASN GLU GLN VAL ASP LYS LEU VAL SER ALA SEQRES 11 B 133 GLY ILE ARG HET F95 A1001 17 HET MN A1002 1 HET MN A1003 1 HET F95 B 601 17 HET MN B 602 1 HET MN B 603 1 HETNAM F95 (7,8-DIHYDROXY-2-OXO-2H-CHROMEN-4-YL)ACETIC ACID HETNAM MN MANGANESE (II) ION FORMUL 3 F95 2(C11 H8 O6) FORMUL 4 MN 4(MN 2+) FORMUL 9 HOH *176(H2 O) HELIX 1 1 THR A 473 SER A 489 1 17 HELIX 2 2 SER A 499 ALA A 508 1 10 HELIX 3 3 SER A 515 LYS A 528 1 14 HELIX 4 4 ILE A 542 ALA A 554 1 13 HELIX 5 5 THR B 473 SER B 489 1 17 HELIX 6 6 SER B 499 ALA B 508 1 10 HELIX 7 7 SER B 515 LYS B 528 1 14 HELIX 8 8 ILE B 542 ALA B 554 1 13 SHEET 1 A 5 GLN A 464 THR A 470 0 SHEET 2 A 5 LEU A 452 THR A 459 -1 N ALA A 455 O VAL A 467 SHEET 3 A 5 THR A 439 ALA A 446 -1 N TYR A 441 O VAL A 458 SHEET 4 A 5 GLU A 492 THR A 497 1 O ASN A 494 N PHE A 440 SHEET 5 A 5 LYS A 530 TRP A 535 1 O ALA A 534 N ILE A 495 SHEET 1 B 5 GLN B 464 LEU B 469 0 SHEET 2 B 5 GLY B 453 THR B 459 -1 N GLY B 453 O LEU B 469 SHEET 3 B 5 THR B 439 ALA B 446 -1 N TYR B 441 O VAL B 458 SHEET 4 B 5 GLU B 492 THR B 497 1 O ASN B 494 N PHE B 440 SHEET 5 B 5 LYS B 530 TRP B 535 1 O TYR B 532 N ILE B 495 LINK O1 F95 A1001 MN MN A1002 1555 1555 1.99 LINK O1 F95 B 601 MN MN B 603 1555 1555 1.99 LINK OE2 GLU A 478 MN MN A1003 1555 1555 2.08 LINK OD2 ASP A 443 MN MN A1003 1555 1555 2.09 LINK OD2 ASP B 443 MN MN B 603 1555 1555 2.11 LINK OD1 ASP A 498 MN MN A1003 1555 1555 2.11 LINK OD1 ASP B 498 MN MN B 603 1555 1555 2.11 LINK OD1 ASP B 549 MN MN B 602 1555 1555 2.12 LINK O1 F95 A1001 MN MN A1003 1555 1555 2.13 LINK OE1 GLU B 478 MN MN B 603 1555 1555 2.14 LINK OD1 ASP A 549 MN MN A1002 1555 1555 2.14 LINK O1 F95 B 601 MN MN B 602 1555 1555 2.14 LINK OD1 ASP B 443 MN MN B 602 1555 1555 2.19 LINK MN MN A1002 O HOH A1112 1555 1555 2.19 LINK MN MN B 602 O HOH B 717 1555 1555 2.19 LINK MN MN B 602 O HOH B 705 1555 1555 2.20 LINK OD1 ASP A 443 MN MN A1002 1555 1555 2.21 LINK MN MN A1002 O HOH A1113 1555 1555 2.21 LINK O2 F95 B 601 MN MN B 602 1555 1555 2.22 LINK O2 F95 A1001 MN MN A1002 1555 1555 2.22 LINK OD2 ASP B 498 MN MN B 603 1555 1555 2.33 LINK OD2 ASP A 498 MN MN A1003 1555 1555 2.40 LINK O3 F95 A1001 MN MN A1003 1555 1555 2.49 LINK O3 F95 B 601 MN MN B 603 1555 1555 2.55 SITE 1 AC1 12 ASP A 443 GLU A 478 ASP A 498 SER A 499 SITE 2 AC1 12 HIS A 539 ASP A 549 MN A1002 MN A1003 SITE 3 AC1 12 HOH A1112 HOH A1113 HOH A1122 HOH A1181 SITE 1 AC2 6 ASP A 443 ASP A 549 F95 A1001 MN A1003 SITE 2 AC2 6 HOH A1112 HOH A1113 SITE 1 AC3 5 ASP A 443 GLU A 478 ASP A 498 F95 A1001 SITE 2 AC3 5 MN A1002 SITE 1 AC4 13 ASP B 443 GLU B 478 ASP B 498 SER B 499 SITE 2 AC4 13 HIS B 539 ASP B 549 MN B 602 MN B 603 SITE 3 AC4 13 HOH B 703 HOH B 705 HOH B 706 HOH B 717 SITE 4 AC4 13 HOH B 718 SITE 1 AC5 6 ASP B 443 ASP B 549 F95 B 601 MN B 603 SITE 2 AC5 6 HOH B 705 HOH B 717 SITE 1 AC6 5 ASP B 443 GLU B 478 ASP B 498 F95 B 601 SITE 2 AC6 5 MN B 602 CRYST1 51.162 51.162 112.097 90.00 90.00 120.00 P 31 6 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 0.019546 0.011285 0.000000 0.00000 SCALE2 0.000000 0.022569 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008921 0.00000