HEADER TRANSFERASE/INHIBITOR 09-OCT-20 7KE0 TITLE HIV-1 INTEGRASE CATALYTIC CORE DOMAIN COMPLEXED WITH ALLOSTERIC TITLE 2 INHIBITOR STP03-0404 COMPND MOL_ID: 1; COMPND 2 MOLECULE: INTEGRASE; COMPND 3 CHAIN: A; COMPND 4 EC: 2.7.7.49; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HUMAN IMMUNODEFICIENCY VIRUS 1; SOURCE 3 ORGANISM_COMMON: HIV-1; SOURCE 4 ORGANISM_TAXID: 11676; SOURCE 5 GENE: POL; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693 KEYWDS INTEGRASE, INHIBITOR, HIV, TRANSFERASE-INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR J.J.LINDENBERGER,M.KVARATSKHELIA REVDAT 3 18-OCT-23 7KE0 1 HETSYN REVDAT 2 06-APR-22 7KE0 1 JRNL REVDAT 1 22-SEP-21 7KE0 0 JRNL AUTH T.MAEHIGASHI,S.AHN,U.I.KIM,J.LINDENBERGER,A.OO,P.C.KONERU, JRNL AUTH 2 B.MAHBOUBI,A.N.ENGELMAN,M.KVARATSKHELIA,K.KIM,B.KIM JRNL TITL A HIGHLY POTENT AND SAFE PYRROLOPYRIDINE-BASED ALLOSTERIC JRNL TITL 2 HIV-1 INTEGRASE INHIBITOR TARGETING HOST LEDGF/P75-INTEGRASE JRNL TITL 3 INTERACTION SITE. JRNL REF PLOS PATHOG. V. 17 09671 2021 JRNL REFN ESSN 1553-7374 JRNL PMID 34293041 JRNL DOI 10.1371/JOURNAL.PPAT.1009671 REMARK 2 REMARK 2 RESOLUTION. 2.19 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.14_3260 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 : CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.19 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 23.55 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 89.0 REMARK 3 NUMBER OF REFLECTIONS : 17510 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.252 REMARK 3 R VALUE (WORKING SET) : 0.250 REMARK 3 FREE R VALUE : 0.269 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.820 REMARK 3 FREE R VALUE TEST SET COUNT : 1719 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 23.5500 - 4.9900 0.96 1436 147 0.2141 0.1925 REMARK 3 2 4.9900 - 3.9700 0.94 1398 148 0.1913 0.1809 REMARK 3 3 3.9700 - 3.4700 0.98 1444 159 0.1995 0.2343 REMARK 3 4 3.4700 - 3.1500 0.90 1322 147 0.2630 0.3183 REMARK 3 5 3.1500 - 2.9300 0.87 1288 142 0.2855 0.2677 REMARK 3 6 2.9300 - 2.7600 0.86 1241 147 0.3076 0.3777 REMARK 3 7 2.7600 - 2.6200 0.87 1314 145 0.3397 0.3696 REMARK 3 8 2.6200 - 2.5000 0.91 1311 150 0.3365 0.3796 REMARK 3 9 2.5000 - 2.4100 0.92 1389 153 0.3401 0.4667 REMARK 3 10 2.4100 - 2.3200 0.95 1387 155 0.3461 0.4455 REMARK 3 11 2.3200 - 2.2500 0.84 1267 134 0.3308 0.3461 REMARK 3 12 2.2500 - 2.1900 0.68 994 92 0.3036 0.4053 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) : 0.355 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 31.848 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 34.83 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 38.00 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 1093 REMARK 3 ANGLE : 0.655 1489 REMARK 3 CHIRALITY : 0.042 164 REMARK 3 PLANARITY : 0.002 180 REMARK 3 DIHEDRAL : 3.582 618 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 7KE0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-OCT-20. REMARK 100 THE DEPOSITION ID IS D_1000252285. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-OCT-18 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) : 1.54178 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 200K REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 1.10.1_2155 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17510 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.187 REMARK 200 RESOLUTION RANGE LOW (A) : 24.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 8.800 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 22.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.19 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.28 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: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 6EB2 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.89 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.67 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M SODIUIM CACODYLATE TRIHYDRATE, REMARK 280 0.1 M AMMONIUM SULFATE, 10% PEG8000, PH 6.5, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 277K 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 21.95667 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 43.91333 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 43.91333 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 21.95667 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: 3030 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11790 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -18.0 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 350 BIOMT1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 -0.866025 0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 -43.91333 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 CYS A 56 REMARK 465 PHE A 139 REMARK 465 GLY A 140 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 LYS A 188 REMARK 465 GLY A 189 REMARK 465 GLY A 190 REMARK 465 ILE A 191 REMARK 465 GLY A 192 REMARK 465 ILE A 208 REMARK 465 GLN A 209 REMARK 465 THR A 210 REMARK 465 LYS A 211 REMARK 465 GLU A 212 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 PRO A 109 86.32 -69.37 REMARK 500 REMARK 500 REMARK: NULL DBREF 7KE0 A 50 212 UNP F2WR52 F2WR52_9HIV1 50 212 SEQADV 7KE0 GLY A 47 UNP F2WR52 EXPRESSION TAG SEQADV 7KE0 SER A 48 UNP F2WR52 EXPRESSION TAG SEQADV 7KE0 HIS A 49 UNP F2WR52 EXPRESSION TAG SEQADV 7KE0 HIS A 185 UNP F2WR52 PHE 185 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 HIS 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 7KE0 CAF A 65 CYS MODIFIED RESIDUE MODRES 7KE0 CAF A 130 CYS MODIFIED RESIDUE HET CAF A 65 10 HET CAF A 130 10 HET WBV A 301 35 HETNAM CAF S-DIMETHYLARSINOYL-CYSTEINE HETNAM WBV (2S)-TERT-BUTOXY{4-(4-CHLOROPHENYL)-2,3,6-TRIMETHYL-1- HETNAM 2 WBV [(1-METHYL-1H-PYRAZOL-4-YL)METHYL]-1H-PYRROLO[2,3- HETNAM 3 WBV B]PYRIDIN-5-YL}ACETIC ACID HETSYN CAF CYSTEIN-S-YL CACODYLATE HETSYN WBV PIRMITEGRAVIR FORMUL 1 CAF 2(C5 H12 AS N O3 S) FORMUL 2 WBV C27 H31 CL N4 O3 FORMUL 3 HOH *29(H2 O) HELIX 1 AA1 THR A 93 TRP A 108 1 16 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 ASP A 207 1 13 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 71.932 71.932 65.870 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 0.013902 0.008026 0.000000 0.00000 SCALE2 0.000000 0.016053 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015181 0.00000