HEADER HYDROLASE/INHIBITOR 15-OCT-22 8ESY TITLE D30N MUTANT HIV PROTEASE IN COMPLEX WITH BENZOXABOROLONE ANALOG OF TITLE 2 DARUNAVIR COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEASE; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES; COMPND 5 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; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS VIRUS, PROTEASE, INHIBITOR, BORON, HYDROLASE, HYDROLASE-INHIBITOR KEYWDS 2 COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR I.W.WINDSOR,B.J.GRAHAM,R.T.RAINES REVDAT 3 25-OCT-23 8ESY 1 REMARK REVDAT 2 01-MAR-23 8ESY 1 JRNL REVDAT 1 08-FEB-23 8ESY 0 JRNL AUTH B.J.GRAHAM,I.W.WINDSOR,R.T.RAINES JRNL TITL INHIBITION OF HIV-1 PROTEASE BY A BORONIC ACID WITH HIGH JRNL TITL 2 OXIDATIVE STABILITY. JRNL REF ACS MED.CHEM.LETT. V. 14 171 2023 JRNL REFN ISSN 1948-5875 JRNL PMID 36793428 JRNL DOI 10.1021/ACSMEDCHEMLETT.2C00464 REMARK 2 REMARK 2 RESOLUTION. 1.35 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1_4487 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.35 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.40 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 52258 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.198 REMARK 3 R VALUE (WORKING SET) : 0.197 REMARK 3 FREE R VALUE : 0.221 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.830 REMARK 3 FREE R VALUE TEST SET COUNT : 2000 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 48.4000 - 3.2500 1.00 3816 152 0.1656 0.1897 REMARK 3 2 3.2500 - 2.5800 1.00 3671 146 0.1970 0.2354 REMARK 3 3 2.5800 - 2.2600 1.00 3638 145 0.2040 0.2283 REMARK 3 4 2.2600 - 2.0500 1.00 3601 142 0.1917 0.1901 REMARK 3 5 2.0500 - 1.9000 1.00 3591 144 0.2046 0.2312 REMARK 3 6 1.9000 - 1.7900 1.00 3572 142 0.1984 0.2279 REMARK 3 7 1.7900 - 1.7000 1.00 3573 142 0.2134 0.2138 REMARK 3 8 1.7000 - 1.6300 1.00 3552 142 0.2316 0.2654 REMARK 3 9 1.6300 - 1.5600 1.00 3559 141 0.2428 0.2753 REMARK 3 10 1.5600 - 1.5100 1.00 3546 142 0.2339 0.2500 REMARK 3 11 1.5100 - 1.4600 1.00 3525 140 0.2381 0.2597 REMARK 3 12 1.4600 - 1.4200 1.00 3576 142 0.2459 0.2823 REMARK 3 13 1.4200 - 1.3800 1.00 3523 141 0.2697 0.3073 REMARK 3 14 1.3800 - 1.3500 0.99 3515 139 0.3432 0.3718 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) : 0.185 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.892 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 18.78 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.07 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 : 0.012 1693 REMARK 3 ANGLE : 1.234 2320 REMARK 3 CHIRALITY : 0.087 273 REMARK 3 PLANARITY : 0.008 280 REMARK 3 DIHEDRAL : 14.800 254 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 8ESY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-NOV-22. REMARK 100 THE DEPOSITION ID IS D_1000269357. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-FEB-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 23-ID-D REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.96862 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 52315 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.350 REMARK 200 RESOLUTION RANGE LOW (A) : 48.400 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 12.30 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL 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) : 1.35 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.39 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.0 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 : 1.330 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: 6C8X REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.09 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.74 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM TRIS PH 7.5 AND 500 MM NACL, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 278K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 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 29.22000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 43.19000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 29.22000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 43.19000 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: 4680 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9640 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -48.0 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 GLN A 18 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 TRP A 6 CZ3 REMARK 480 ARG B 108 CZ DBREF 8ESY A 1 99 UNP Q5RZ08 Q5RZ08_9HIV1 1 99 DBREF 8ESY B 101 199 UNP Q5RZ08 Q5RZ08_9HIV1 1 99 SEQADV 8ESY LYS A 7 UNP Q5RZ08 GLN 7 ENGINEERED MUTATION SEQADV 8ESY ASN A 30 UNP Q5RZ08 ASP 30 ENGINEERED MUTATION SEQADV 8ESY ILE A 33 UNP Q5RZ08 LEU 33 ENGINEERED MUTATION SEQADV 8ESY ILE A 63 UNP Q5RZ08 LEU 63 ENGINEERED MUTATION SEQADV 8ESY ALA A 67 UNP Q5RZ08 CYS 67 ENGINEERED MUTATION SEQADV 8ESY ALA A 95 UNP Q5RZ08 CYS 95 ENGINEERED MUTATION SEQADV 8ESY LYS B 107 UNP Q5RZ08 GLN 7 ENGINEERED MUTATION SEQADV 8ESY ASN B 130 UNP Q5RZ08 ASP 30 ENGINEERED MUTATION SEQADV 8ESY ILE B 133 UNP Q5RZ08 LEU 33 ENGINEERED MUTATION SEQADV 8ESY ILE B 163 UNP Q5RZ08 LEU 63 ENGINEERED MUTATION SEQADV 8ESY ALA B 167 UNP Q5RZ08 CYS 67 ENGINEERED MUTATION SEQADV 8ESY ALA B 195 UNP Q5RZ08 CYS 95 ENGINEERED MUTATION SEQRES 1 A 99 PRO GLN ILE THR LEU TRP LYS ARG PRO LEU VAL THR ILE SEQRES 2 A 99 LYS ILE GLY GLY GLN LEU LYS GLU ALA LEU LEU ASP THR SEQRES 3 A 99 GLY ALA ASP ASN THR VAL ILE GLU GLU MET SER LEU PRO SEQRES 4 A 99 GLY ARG TRP LYS PRO LYS MET ILE GLY GLY ILE GLY GLY SEQRES 5 A 99 PHE ILE LYS VAL ARG GLN TYR ASP GLN ILE ILE ILE GLU SEQRES 6 A 99 ILE ALA GLY HIS LYS ALA ILE GLY THR VAL LEU VAL GLY SEQRES 7 A 99 PRO THR PRO VAL ASN ILE ILE GLY ARG ASN LEU LEU THR SEQRES 8 A 99 GLN ILE GLY ALA THR LEU ASN PHE SEQRES 1 B 99 PRO GLN ILE THR LEU TRP LYS ARG PRO LEU VAL THR ILE SEQRES 2 B 99 LYS ILE GLY GLY GLN LEU LYS GLU ALA LEU LEU ASP THR SEQRES 3 B 99 GLY ALA ASP ASN THR VAL ILE GLU GLU MET SER LEU PRO SEQRES 4 B 99 GLY ARG TRP LYS PRO LYS MET ILE GLY GLY ILE GLY GLY SEQRES 5 B 99 PHE ILE LYS VAL ARG GLN TYR ASP GLN ILE ILE ILE GLU SEQRES 6 B 99 ILE ALA GLY HIS LYS ALA ILE GLY THR VAL LEU VAL GLY SEQRES 7 B 99 PRO THR PRO VAL ASN ILE ILE GLY ARG ASN LEU LEU THR SEQRES 8 B 99 GLN ILE GLY ALA THR LEU ASN PHE HET GOL A 101 6 HET CL A 102 1 HET X7B B 201 86 HET CL B 202 1 HET CL B 203 1 HETNAM GOL GLYCEROL HETNAM CL CHLORIDE ION HETNAM X7B [(3~{A}~{S},4~{R},6~{A}~{R})-2,3,3~{A},4,5,6~{A}- HETNAM 2 X7B HEXAHYDROFURO[2,3-B]FURAN-4-YL] ~{N}-[(2~{S},3~{R})-4- HETNAM 3 X7B [[7,7-BIS(OXIDANYL)-9-OXIDANYLIDENE-8-OXA-7- HETNAM 4 X7B BORANUIDABICYCLO[4.3.0]NONA-1,3,5-TRIEN-3-YL]SULFONYL- HETNAM 5 X7B (2-METHYLPROPYL)AMINO]-3-OXIDANYL-1-PHENYL-BUTAN-2- HETNAM 6 X7B YL]CARBAMATE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 GOL C3 H8 O3 FORMUL 4 CL 3(CL 1-) FORMUL 5 X7B C28 H36 B N2 O11 S 1- FORMUL 8 HOH *225(H2 O) HELIX 1 AA1 GLY A 86 THR A 91 1 6 HELIX 2 AA2 GLY B 186 ILE B 193 1 8 SHEET 1 AA1 4 GLN A 2 ILE A 3 0 SHEET 2 AA1 4 THR B 196 ASN B 198 -1 O LEU B 197 N ILE A 3 SHEET 3 AA1 4 THR A 96 ASN A 98 -1 N ASN A 98 O THR B 196 SHEET 4 AA1 4 GLN B 102 ILE B 103 -1 O ILE B 103 N LEU A 97 SHEET 1 AA2 8 TRP A 42 GLY A 49 0 SHEET 2 AA2 8 GLY A 52 ILE A 66 -1 O GLN A 58 N LYS A 43 SHEET 3 AA2 8 HIS A 69 VAL A 77 -1 O HIS A 69 N ILE A 66 SHEET 4 AA2 8 THR A 31 ILE A 33 1 N ILE A 33 O LEU A 76 SHEET 5 AA2 8 ILE A 84 ILE A 85 -1 O ILE A 84 N VAL A 32 SHEET 6 AA2 8 LYS A 20 LEU A 24 1 N LEU A 23 O ILE A 85 SHEET 7 AA2 8 LEU A 10 ILE A 15 -1 N ILE A 13 O LYS A 20 SHEET 8 AA2 8 GLY A 52 ILE A 66 -1 O GLU A 65 N LYS A 14 SHEET 1 AA3 8 LYS B 143 GLY B 149 0 SHEET 2 AA3 8 GLY B 152 ILE B 166 -1 O GLN B 158 N LYS B 143 SHEET 3 AA3 8 HIS B 169 VAL B 177 -1 O HIS B 169 N ILE B 166 SHEET 4 AA3 8 VAL B 132 ILE B 133 1 N ILE B 133 O LEU B 176 SHEET 5 AA3 8 ILE B 184 ILE B 185 -1 O ILE B 184 N VAL B 132 SHEET 6 AA3 8 GLN B 118 LEU B 124 1 N LEU B 123 O ILE B 185 SHEET 7 AA3 8 LEU B 110 ILE B 115 -1 N ILE B 113 O LYS B 120 SHEET 8 AA3 8 GLY B 152 ILE B 166 -1 O GLU B 165 N LYS B 114 CRYST1 58.440 86.380 46.340 90.00 90.00 90.00 P 21 21 2 8 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 0.017112 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011577 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021580 0.00000