HEADER TRANSFERASE/TRANSFERASE INHIBITOR 01-FEB-19 6NUJ TITLE HIV-1 INTEGRASE CATALYTIC CORE DOMAIN COMPLEXED WITH ALLOSTERIC TITLE 2 INHIBITOR BI-224436 COMPND MOL_ID: 1; COMPND 2 MOLECULE: INTEGRASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: CCD (UNP RESIDUES 50-212); COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HUMAN IMMUNODEFICIENCY VIRUS 1; SOURCE 3 ORGANISM_TAXID: 11676; SOURCE 4 GENE: POL; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 511693 KEYWDS HIV, INTEGRASE, INHIBITOR, ALLOSTERIC, TRANSFERASE-TRANSFERASE KEYWDS 2 INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR J.J.LINDENBERGER,M.KVARATSKHELIA REVDAT 2 11-OCT-23 6NUJ 1 REMARK REVDAT 1 11-DEC-19 6NUJ 0 JRNL AUTH P.C.KONERU,A.C.FRANCIS,N.DENG,S.V.REBENSBURG,A.C.HOYTE, JRNL AUTH 2 J.LINDENBERGER,D.ADU-AMPRATWUM,R.C.LARUE,M.F.WEMPE, JRNL AUTH 3 A.N.ENGELMAN,D.LYUMKIS,J.R.FUCHS,R.M.LEVY,G.B.MELIKYAN, JRNL AUTH 4 M.KVARATSKHELIA JRNL TITL HIV-1 INTEGRASE TETRAMERS ARE THE ANTIVIRAL TARGET OF JRNL TITL 2 PYRIDINE-BASED ALLOSTERIC INTEGRASE INHIBITORS. JRNL REF ELIFE V. 8 2019 JRNL REFN ESSN 2050-084X JRNL PMID 31120420 JRNL DOI 10.7554/ELIFE.46344 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.10.1_2155 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) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.37 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.335 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.5 REMARK 3 NUMBER OF REFLECTIONS : 11892 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.222 REMARK 3 R VALUE (WORKING SET) : 0.219 REMARK 3 FREE R VALUE : 0.244 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.011 REMARK 3 FREE R VALUE TEST SET COUNT : 2155 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 24.3761 - 5.1637 1.00 1341 148 0.2083 0.2374 REMARK 3 2 5.1637 - 4.1050 0.99 1357 146 0.1795 0.1566 REMARK 3 3 4.1050 - 3.5879 0.99 1340 146 0.1916 0.1926 REMARK 3 4 3.5879 - 3.2607 0.99 1333 145 0.2065 0.2739 REMARK 3 5 3.2607 - 3.0275 0.98 1345 148 0.2276 0.2363 REMARK 3 6 3.0275 - 2.8493 0.97 1302 143 0.2346 0.2613 REMARK 3 7 2.8493 - 2.7068 0.98 1345 144 0.2445 0.2720 REMARK 3 8 2.7068 - 2.5891 0.97 1312 135 0.2668 0.2885 REMARK 3 9 2.5891 - 2.4895 0.98 1285 153 0.2422 0.4318 REMARK 3 10 2.4895 - 2.4037 0.98 1339 144 0.2395 0.2330 REMARK 3 11 2.4037 - 2.3286 0.99 1304 155 0.2477 0.2850 REMARK 3 12 2.3286 - 2.2621 0.99 1349 156 0.2428 0.2768 REMARK 3 13 2.2621 - 2.2026 0.94 1258 146 0.2435 0.3123 REMARK 3 14 2.2026 - 2.1488 0.85 1148 131 0.2312 0.2509 REMARK 3 15 2.1488 - 2.1000 0.73 1013 115 0.2469 0.2717 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) : 0.203 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.262 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 22.82 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.11 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 : 0.002 1087 REMARK 3 ANGLE : 0.665 1481 REMARK 3 CHIRALITY : 0.045 165 REMARK 3 PLANARITY : 0.003 177 REMARK 3 DIHEDRAL : 15.831 613 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 6NUJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-FEB-19. REMARK 100 THE DEPOSITION ID IS D_1000239448. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-DEC-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 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12002 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 24.374 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 14.60 REMARK 200 R MERGE (I) : 0.05141 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 61.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.17 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.27560 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 9.040 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 (%): 49.71 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.45 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M SODIUM 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 22.02633 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 44.05267 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 44.05267 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 22.02633 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: 3500 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11700 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -21.0 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 -44.05267 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 GLU A 138 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 GLY A 193 REMARK 465 GLN A 209 REMARK 465 THR A 210 REMARK 465 LYS A 211 REMARK 465 GLU A 212 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue L3D A 300 DBREF 6NUJ A 50 212 UNP F2WR52 F2WR52_9HIV1 50 212 SEQADV 6NUJ GLY A 47 UNP F2WR52 EXPRESSION TAG SEQADV 6NUJ SER A 48 UNP F2WR52 EXPRESSION TAG SEQADV 6NUJ HIS A 49 UNP F2WR52 EXPRESSION TAG SEQADV 6NUJ 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 6NUJ CAF A 65 CYS MODIFIED RESIDUE MODRES 6NUJ CAF A 130 CYS MODIFIED RESIDUE HET CAF A 65 10 HET CAF A 130 10 HET L3D A 300 33 HETNAM CAF S-DIMETHYLARSINOYL-CYSTEINE HETNAM L3D (2S)-TERT-BUTOXY[4-(2,3-DIHYDROPYRANO[4,3,2- HETNAM 2 L3D DE]QUINOLIN-7-YL)-2-METHYLQUINOLIN-3-YL]ACETIC ACID HETSYN CAF CYSTEIN-S-YL CACODYLATE FORMUL 1 CAF 2(C5 H12 AS N O3 S) FORMUL 2 L3D C27 H26 N2 O4 FORMUL 3 HOH *53(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 ILE A 208 1 14 SHEET 1 AA1 4 ILE A 84 ILE A 89 0 SHEET 2 AA1 4 LYS A 71 HIS A 78 -1 N ALA A 76 O GLU A 85 SHEET 3 AA1 4 ILE A 60 LEU A 68 -1 N ASP A 64 O VAL A 75 SHEET 4 AA1 4 THR A 112 HIS A 114 1 O HIS A 114 N TRP A 61 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 SITE 1 AC1 11 LEU A 102 ALA A 128 ALA A 129 TRP A 132 SITE 2 AC1 11 GLN A 168 GLU A 170 HIS A 171 THR A 174 SITE 3 AC1 11 MET A 178 HOH A 430 HOH A 438 CRYST1 72.211 72.211 66.079 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 0.013848 0.007995 0.000000 0.00000 SCALE2 0.000000 0.015991 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015133 0.00000