HEADER HYDROLASE 20-DEC-21 7WCE TITLE CRYSTAL STRUCTURE OF HIV-1 INTEGRASE CATALYTIC CORE DOMAIN IN COMPLEX TITLE 2 WITH (2S)-2-(TERT-BUTOXY)-2-(10-FLUORO-2-(2-HYDROXY-4-METHYLPHENYL)- TITLE 3 1,4-DIMETHYL-5-(METHYLSULFONYL)-5,6-DIHYDROPHENANTHRIDIN-3-YL)ACETIC TITLE 4 ACID COMPND MOL_ID: 1; COMPND 2 MOLECULE: INTEGRASE CATALYTIC; COMPND 3 CHAIN: A; COMPND 4 EC: 3.4.23.16,2.7.7.49,2.7.7.7,3.1.26.13,3.1.13.2,2.7.7.-,3.1.-.-; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HUMAN IMMUNODEFICIENCY VIRUS TYPE 1 (NEW YORK-5 SOURCE 3 ISOLATE); SOURCE 4 ORGANISM_TAXID: 11698; SOURCE 5 STRAIN: ISOLATE NY5; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS HIV-1 INTEGRASE, VIRAL PROTEIN, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR Y.TAODA,Y.SEKIGUCHI REVDAT 3 30-OCT-24 7WCE 1 REMARK REVDAT 2 29-NOV-23 7WCE 1 REMARK REVDAT 1 07-SEP-22 7WCE 0 JRNL AUTH Y.TAODA,T.AKIYAMA,K.TOMITA,M.FUJIWARA-KITAMURA,Y.TAMURA, JRNL AUTH 2 T.KAWASUJI,E.MATSUOKA,E.AKIHISA,T.SEKI,T.YOSHINAGA JRNL TITL DISCOVERY OF TRICYCLIC HIV-1 INTEGRASE-LEDGF/P75 ALLOSTERIC JRNL TITL 2 INHIBITORS BY INTRAMOLECULAR DIRECT ARYLATION REACTION. JRNL REF BIOORG.MED.CHEM.LETT. V. 64 28664 2022 JRNL REFN ESSN 1464-3405 JRNL PMID 35272008 JRNL DOI 10.1016/J.BMCL.2022.128664 REMARK 2 REMARK 2 RESOLUTION. 1.85 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX V1.11.1-2575 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) : 1.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 22.69 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 17387 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.194 REMARK 3 R VALUE (WORKING SET) : 0.193 REMARK 3 FREE R VALUE : 0.214 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.060 REMARK 3 FREE R VALUE TEST SET COUNT : 880 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 22.6920 - 3.3579 1.00 2869 148 0.1811 0.2022 REMARK 3 2 3.3579 - 2.6666 1.00 2775 130 0.1941 0.1988 REMARK 3 3 2.6666 - 2.3299 1.00 2721 151 0.2002 0.2395 REMARK 3 4 2.3299 - 2.1171 1.00 2712 173 0.2006 0.2129 REMARK 3 5 2.1171 - 1.9654 1.00 2731 133 0.2106 0.2504 REMARK 3 6 1.9654 - 1.8500 1.00 2699 145 0.2482 0.2920 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) : 0.190 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.440 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 42.60 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 : 0.004 1162 REMARK 3 ANGLE : 0.962 1580 REMARK 3 CHIRALITY : 0.061 172 REMARK 3 PLANARITY : 0.003 189 REMARK 3 DIHEDRAL : 16.620 408 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): -23.6024 30.0139 3.2680 REMARK 3 T TENSOR REMARK 3 T11: 0.2389 T22: 0.2130 REMARK 3 T33: 0.1973 T12: -0.0219 REMARK 3 T13: -0.0482 T23: 0.0091 REMARK 3 L TENSOR REMARK 3 L11: 2.6813 L22: 1.4585 REMARK 3 L33: 1.6713 L12: 1.2558 REMARK 3 L13: -0.0726 L23: 0.0180 REMARK 3 S TENSOR REMARK 3 S11: -0.2230 S12: 0.2035 S13: 0.1135 REMARK 3 S21: -0.3007 S22: 0.1077 S23: 0.1071 REMARK 3 S31: -0.0305 S32: -0.0269 S33: -0.0053 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 7WCE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 28-DEC-21. REMARK 100 THE DEPOSITION ID IS D_1300026229. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-DEC-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-007 HF REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV++ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17409 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.850 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 6.300 REMARK 200 R MERGE (I) : 0.04500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 23.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.85 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.88 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.3 REMARK 200 DATA REDUNDANCY IN SHELL : 6.10 REMARK 200 R MERGE FOR SHELL (I) : 0.42800 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: MOLREP REMARK 200 STARTING MODEL: 3LPT REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.44 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.70 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M SODIUM CACODYLATE PH 6.5, 0.23 M REMARK 280 AMMONIUM SULFATE, 6% PEG 8000, 5 MM DTT, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 293.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 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 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 21.92533 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 43.85067 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 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 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 43.85067 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 21.92533 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 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 47 REMARK 465 SER A 48 REMARK 465 HIS A 49 REMARK 465 MET A 50 REMARK 465 HIS A 51 REMARK 465 GLY A 52 REMARK 465 GLN A 53 REMARK 465 VAL A 54 REMARK 465 ASP A 55 REMARK 465 ILE A 141 REMARK 465 PRO A 142 REMARK 465 TYR A 143 REMARK 465 ASN A 144 REMARK 465 PRO A 145 REMARK 465 GLN A 146 REMARK 465 SER A 147 REMARK 465 GLN A 148 REMARK 465 GLY A 149 REMARK 465 VAL A 150 REMARK 465 ILE A 151 REMARK 465 GLU A 152 REMARK 465 GLY A 189 REMARK 465 GLY A 190 REMARK 465 ILE A 191 REMARK 465 GLY A 192 REMARK 465 THR A 210 REMARK 465 LYS A 211 REMARK 465 GLU A 212 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 CAF A 65 CE2 REMARK 470 CAF A 130 CE2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH A 451 O HOH A 474 1.62 REMARK 500 OE1 GLU A 138 O HOH A 401 1.96 REMARK 500 O CYS A 56 O HOH A 402 2.03 REMARK 500 OD1 ASP A 167 O HOH A 403 2.03 REMARK 500 O1 GOL A 304 O HOH A 404 2.06 REMARK 500 O HOH A 456 O HOH A 472 2.13 REMARK 500 REMARK 500 REMARK: NULL DBREF 7WCE A 50 212 UNP P12497 POL_HV1N5 1197 1359 SEQADV 7WCE GLY A 47 UNP P12497 EXPRESSION TAG SEQADV 7WCE SER A 48 UNP P12497 EXPRESSION TAG SEQADV 7WCE HIS A 49 UNP P12497 EXPRESSION TAG SEQADV 7WCE LYS A 185 UNP P12497 PHE 1332 ENGINEERED MUTATION SEQRES 1 A 166 GLY SER HIS MET HIS GLY GLN VAL ASP CYS SER PRO GLY SEQRES 2 A 166 ILE TRP GLN LEU ASP CAF THR HIS LEU GLU GLY LYS VAL SEQRES 3 A 166 ILE LEU VAL ALA VAL HIS VAL ALA SER GLY TYR ILE GLU SEQRES 4 A 166 ALA GLU VAL ILE PRO ALA GLU THR GLY GLN GLU THR ALA SEQRES 5 A 166 TYR PHE LEU LEU LYS LEU ALA GLY ARG TRP PRO VAL LYS SEQRES 6 A 166 THR VAL HIS THR ASP ASN GLY SER ASN PHE THR SER THR SEQRES 7 A 166 THR VAL LYS ALA ALA CAF TRP TRP ALA GLY ILE LYS GLN SEQRES 8 A 166 GLU PHE GLY ILE PRO TYR ASN PRO GLN SER GLN GLY VAL SEQRES 9 A 166 ILE GLU SER MET ASN LYS GLU LEU LYS LYS ILE ILE GLY SEQRES 10 A 166 GLN VAL ARG ASP GLN ALA GLU HIS LEU LYS THR ALA VAL SEQRES 11 A 166 GLN MET ALA VAL PHE ILE HIS ASN LYS LYS ARG LYS GLY SEQRES 12 A 166 GLY ILE GLY GLY TYR SER ALA GLY GLU ARG ILE VAL ASP SEQRES 13 A 166 ILE ILE ALA THR ASP ILE GLN THR LYS GLU MODRES 7WCE CAF A 65 CYS MODIFIED RESIDUE MODRES 7WCE CAF A 130 CYS MODIFIED RESIDUE HET CAF A 65 9 HET CAF A 130 9 HET SO4 A 301 5 HET SO4 A 302 5 HET 8Z3 A 303 38 HET GOL A 304 6 HETNAM CAF S-DIMETHYLARSINOYL-CYSTEINE HETNAM SO4 SULFATE ION HETNAM 8Z3 (2S)-2-[10-FLUORANYL-1,4-DIMETHYL-2-(4-METHYL-2- HETNAM 2 8Z3 OXIDANYL-PHENYL)-5-METHYLSULFONYL-6H-PHENANTHRIDIN-3- HETNAM 3 8Z3 YL]-2-[(2-METHYLPROPAN-2-YL)OXY]ETHANOIC ACID HETNAM GOL GLYCEROL HETSYN CAF CYSTEIN-S-YL CACODYLATE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 1 CAF 2(C5 H12 AS N O3 S) FORMUL 2 SO4 2(O4 S 2-) FORMUL 4 8Z3 C29 H32 F N O6 S FORMUL 5 GOL C3 H8 O3 FORMUL 6 HOH *77(H2 O) HELIX 1 AA1 THR A 93 GLY A 106 1 14 HELIX 2 AA2 ASN A 117 THR A 122 5 6 HELIX 3 AA3 SER A 123 GLY A 134 1 12 HELIX 4 AA4 MET A 154 ARG A 166 1 13 HELIX 5 AA5 ASP A 167 ALA A 169 5 3 HELIX 6 AA6 HIS A 171 LYS A 186 1 16 HELIX 7 AA7 SER A 195 GLN A 209 1 15 SHEET 1 AA1 5 ILE A 84 ILE A 89 0 SHEET 2 AA1 5 LYS A 71 HIS A 78 -1 N ALA A 76 O GLU A 85 SHEET 3 AA1 5 ILE A 60 LEU A 68 -1 N ASP A 64 O VAL A 75 SHEET 4 AA1 5 THR A 112 HIS A 114 1 O HIS A 114 N TRP A 61 SHEET 5 AA1 5 LYS A 136 GLN A 137 1 O LYS A 136 N VAL A 113 LINK C ASP A 64 N CAF A 65 1555 1555 1.33 LINK C CAF A 65 N THR A 66 1555 1555 1.33 LINK C ALA A 129 N CAF A 130 1555 1555 1.33 LINK C CAF A 130 N TRP A 131 1555 1555 1.33 CRYST1 72.401 72.401 65.776 90.00 90.00 120.00 P 31 2 1 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 0.013812 0.007974 0.000000 0.00000 SCALE2 0.000000 0.015949 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015203 0.00000