HEADER HYDROLASE/HYDROLASE INHIBITOR 01-JUN-16 5KAO TITLE CRYSTAL STRUCTURE OF WILD TYPE HIV-1 PROTEASE IN COMPLEX WITH GRL- TITLE 2 10413 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 GRL-10413, HIV-1 PROTEASE, PROTEASE-INHIBITOR, DARUNAVIR, 2- KEYWDS 2 CHLOROANISOLE, NONPEPTIDIC, HYDROLASE-HYDROLASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR R.S.YEDIDI,N.S.DELINO,D.DAS,J.D.KAUFMAN,P.T.WINGFIELD,A.K.GHOSH, AUTHOR 2 H.MITSUYA REVDAT 6 27-SEP-23 5KAO 1 REMARK REVDAT 5 04-DEC-19 5KAO 1 SEQADV REVDAT 4 27-SEP-17 5KAO 1 JRNL REVDAT 3 07-DEC-16 5KAO 1 JRNL REVDAT 2 28-SEP-16 5KAO 1 JRNL REVDAT 1 31-AUG-16 5KAO 0 JRNL AUTH M.AMANO,P.M.SALCEDO-GOMEZ,R.ZHAO,R.S.YEDIDI,D.DAS,H.BULUT, JRNL AUTH 2 N.S.DELINO,V.R.SHERI,A.K.GHOSH,H.MITSUYA JRNL TITL A MODIFIED P1 MOIETY ENHANCES IN VITRO ANTIVIRAL ACTIVITY JRNL TITL 2 AGAINST VARIOUS MULTIDRUG-RESISTANT HIV-1 VARIANTS AND IN JRNL TITL 3 VITRO CENTRAL NERVOUS SYSTEM PENETRATION PROPERTIES OF A JRNL TITL 4 NOVEL NONPEPTIDIC PROTEASE INHIBITOR, GRL-10413. JRNL REF ANTIMICROB.AGENTS CHEMOTHER. V. 60 7046 2016 JRNL REFN ESSN 1098-6596 JRNL PMID 27620483 JRNL DOI 10.1128/AAC.01428-16 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.37 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.230 REMARK 3 COMPLETENESS FOR RANGE (%) : 89.8 REMARK 3 NUMBER OF REFLECTIONS : 15506 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.186 REMARK 3 R VALUE (WORKING SET) : 0.184 REMARK 3 FREE R VALUE : 0.221 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.090 REMARK 3 FREE R VALUE TEST SET COUNT : 789 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 3.2699 - 2.5958 0.89 2443 119 0.1961 0.2181 REMARK 3 2 2.5958 - 2.2677 0.91 2459 130 0.1853 0.2338 REMARK 3 3 2.2677 - 2.0604 0.92 2459 136 0.1708 0.2312 REMARK 3 4 2.0604 - 1.9128 0.92 2483 142 0.1782 0.2463 REMARK 3 5 1.9128 - 1.8000 0.93 2476 150 0.1905 0.2596 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) : 0.170 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.930 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.61 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 1594 REMARK 3 ANGLE : 1.203 2167 REMARK 3 CHIRALITY : 0.052 257 REMARK 3 PLANARITY : 0.006 266 REMARK 3 DIHEDRAL : 14.433 590 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 5KAO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-JUN-16. REMARK 100 THE DEPOSITION ID IS D_1000221963. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-NOV-14 REMARK 200 TEMPERATURE (KELVIN) : 95 REMARK 200 PH : 5.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX-300 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18748 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.680 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 (%) : 89.4 REMARK 200 DATA REDUNDANCY : 2.100 REMARK 200 R MERGE (I) : 0.09300 REMARK 200 R SYM (I) : 0.09300 REMARK 200 FOR THE DATA SET : 8.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.68 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.71 REMARK 200 COMPLETENESS FOR SHELL (%) : 75.6 REMARK 200 DATA REDUNDANCY IN SHELL : 1.50 REMARK 200 R MERGE FOR SHELL (I) : 0.33100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.795 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP 10.2.35 REMARK 200 STARTING MODEL: 4HLA REMARK 200 REMARK 200 REMARK: ROD SHAPE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.31 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.10 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M CITRIC ACID BUFFER AT PH 5.0 REMARK 280 WITH AMMONIUM SULFATE AS PRECIPITANT, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 25.32500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 30.77900 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 28.83750 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 30.77900 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 25.32500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 28.83750 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: 4020 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9460 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: 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 668 O HOH B 163 1.82 REMARK 500 O HOH B 137 O HOH B 164 2.00 REMARK 500 O HOH A 650 O HOH A 659 2.03 REMARK 500 O ILE B 50 O HOH B 101 2.04 REMARK 500 O HOH A 627 O HOH A 660 2.06 REMARK 500 O HOH A 637 O HOH A 653 2.11 REMARK 500 O HOH A 634 O HOH B 161 2.13 REMARK 500 O HOH A 616 O HOH A 669 2.15 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue G43 A 500 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4HLA RELATED DB: PDB REMARK 900 WILD TYPE HIV-1 PROTEASE IN COMPLEX WITH DARUNAVIR DBREF 5KAO A 1 99 UNP Q72874 Q72874_9HIV1 1 99 DBREF 5KAO B 1 99 UNP Q72874 Q72874_9HIV1 1 99 SEQADV 5KAO ALA A 67 UNP Q72874 CYS 67 ENGINEERED MUTATION SEQADV 5KAO ALA A 95 UNP Q72874 CYS 95 ENGINEERED MUTATION SEQADV 5KAO ALA B 67 UNP Q72874 CYS 67 ENGINEERED MUTATION SEQADV 5KAO ALA B 95 UNP Q72874 CYS 95 ENGINEERED MUTATION SEQRES 1 A 99 PRO GLN VAL THR LEU TRP GLN 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 ASP THR VAL LEU 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 LEU 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 VAL THR LEU TRP GLN 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 ASP THR VAL LEU 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 LEU 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 G43 A 500 50 HETNAM G43 [(3~{A}~{S},4~{R},6~{A}~{R})-2,3,3~{A},4,5,6~{A}- HETNAM 2 G43 HEXAHYDROFURO[2,3-B]FURAN-4-YL] ~{N}-[(2~{S},3~{R})-1- HETNAM 3 G43 (3-CHLORANYL-4-METHOXY-PHENYL)-4-[(4-METHOXYPHENYL) HETNAM 4 G43 SULFONYL-(2-METHYLPROPYL)AMINO]-3-OXIDANYL-BUTAN-2- HETNAM 5 G43 YL]CARBAMATE FORMUL 3 G43 C29 H39 CL N2 O9 S FORMUL 4 HOH *140(H2 O) HELIX 1 AA1 GLY A 86 THR A 91 1 6 HELIX 2 AA2 GLY B 86 THR B 91 1 6 HELIX 3 AA3 GLN B 92 GLY B 94 5 3 SHEET 1 AA1 4 GLN A 2 VAL A 3 0 SHEET 2 AA1 4 THR B 96 ASN B 98 -1 O LEU B 97 N VAL A 3 SHEET 3 AA1 4 THR A 96 ASN A 98 -1 N THR A 96 O ASN B 98 SHEET 4 AA1 4 GLN B 2 VAL B 3 -1 O VAL B 3 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 VAL A 32 LEU A 33 1 N LEU 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 GLN A 18 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 43 GLY B 49 0 SHEET 2 AA3 8 GLY B 52 ILE B 66 -1 O VAL B 56 N LYS B 45 SHEET 3 AA3 8 HIS B 69 GLY B 78 -1 O HIS B 69 N ILE B 66 SHEET 4 AA3 8 THR B 31 GLU B 34 1 N LEU B 33 O LEU B 76 SHEET 5 AA3 8 ASN B 83 ILE B 85 -1 O ILE B 84 N VAL B 32 SHEET 6 AA3 8 GLN B 18 LEU B 24 1 N LEU B 23 O ILE B 85 SHEET 7 AA3 8 LEU B 10 ILE B 15 -1 N VAL B 11 O ALA B 22 SHEET 8 AA3 8 GLY B 52 ILE B 66 -1 O GLU B 65 N LYS B 14 SITE 1 AC1 21 ASP A 25 GLY A 27 ALA A 28 ASP A 29 SITE 2 AC1 21 ASP A 30 GLY A 48 GLY A 49 ILE A 50 SITE 3 AC1 21 VAL A 82 HOH A 618 ARG B 8 LEU B 23 SITE 4 AC1 21 ASP B 25 GLY B 27 ALA B 28 ASP B 30 SITE 5 AC1 21 GLY B 48 GLY B 49 PRO B 81 VAL B 82 SITE 6 AC1 21 ILE B 84 CRYST1 50.650 57.675 61.558 90.00 90.00 90.00 P 21 21 21 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 0.019743 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017339 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016245 0.00000