HEADER HYDROLASE/HYDROLASE INHIBITOR 25-APR-19 6OPT TITLE HIV-1 PROTEASE NL4-3 V82F, I84V MUTANT IN COMPLEX WITH DARUNAVIR COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEASE NL4-3; COMPND 3 CHAIN: B, A; 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; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PXC35 KEYWDS HIV, NL4-3 PROTEASE, DRUG RESISTANCE, PROTEASE INHIBITOR, HYDROLASE KEYWDS 2 INHIBITOR COMPLEX, HYDROLASE, HYDROLASE-HYDROLASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR G.J.LOCKBAUM,M.HENES,K.KOSOVRASTI,F.LEIDNER,G.S.NACHUM,E.A.NALIVAIKA, AUTHOR 2 D.N.A.BOLON,N.KURTYILMAZ,C.A.SCHIFFER REVDAT 4 11-OCT-23 6OPT 1 HETSYN REVDAT 3 01-JAN-20 6OPT 1 REMARK REVDAT 2 27-NOV-19 6OPT 1 JRNL REVDAT 1 04-SEP-19 6OPT 0 JRNL AUTH M.HENES,G.J.LOCKBAUM,K.KOSOVRASTI,F.LEIDNER,G.S.NACHUM, JRNL AUTH 2 E.A.NALIVAIKA,S.K.LEE,E.SPIELVOGEL,S.ZHOU,R.SWANSTROM, JRNL AUTH 3 D.N.A.BOLON,N.KURT YILMAZ,C.A.SCHIFFER JRNL TITL PICOMOLAR TO MICROMOLAR: ELUCIDATING THE ROLE OF DISTAL JRNL TITL 2 MUTATIONS IN HIV-1 PROTEASE IN CONFERRING DRUG RESISTANCE. JRNL REF ACS CHEM.BIOL. V. 14 2441 2019 JRNL REFN ESSN 1554-8937 JRNL PMID 31361460 JRNL DOI 10.1021/ACSCHEMBIO.9B00370 REMARK 2 REMARK 2 RESOLUTION. 1.96 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.12-2829 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) : 1.96 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.43 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.6 REMARK 3 NUMBER OF REFLECTIONS : 13072 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.185 REMARK 3 R VALUE (WORKING SET) : 0.182 REMARK 3 FREE R VALUE : 0.228 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.020 REMARK 3 FREE R VALUE TEST SET COUNT : 656 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 32.4366 - 3.3510 0.99 2668 144 0.1668 0.2091 REMARK 3 2 3.3510 - 2.6602 0.98 2510 132 0.1867 0.2148 REMARK 3 3 2.6602 - 2.3240 0.97 2473 132 0.1937 0.2521 REMARK 3 4 2.3240 - 2.1116 0.96 2426 118 0.1995 0.2708 REMARK 3 5 2.1116 - 1.9603 0.93 2339 130 0.2154 0.2669 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) : 0.230 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.870 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 1575 REMARK 3 ANGLE : 0.663 2143 REMARK 3 CHIRALITY : 0.051 251 REMARK 3 PLANARITY : 0.003 266 REMARK 3 DIHEDRAL : 13.993 914 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 6OPT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-APR-19. REMARK 100 THE DEPOSITION ID IS D_1000241134. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-MAR-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL 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 : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU SATURN 944 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : HKL-3000 V703X REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13103 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.960 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 (%) : 96.5 REMARK 200 DATA REDUNDANCY : 19.30 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 53.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.96 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.11 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: 6DH0 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.85 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.08 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 19-26% (W/V) AMMONIUM SULFATE, 0.1M REMARK 280 BIS-TRIS-METHANE-HCL BUFFER PH 5.5, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 293K 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 25.38700 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 30.77150 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 28.92600 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 30.77150 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 25.38700 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 28.92600 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: 5130 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9290 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -53.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, 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 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 LYS B 14 CG CD CE NZ REMARK 470 LYS B 43 CG CD CE NZ REMARK 470 LEU B 63 CG CD1 CD2 REMARK 470 ARG A 41 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 43 CG CD CE NZ REMARK 470 LYS A 45 CG CD CE NZ REMARK 470 LEU A 63 CG CD1 CD2 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 260 O HOH A 270 1.99 REMARK 500 O HOH A 252 O HOH A 276 2.01 REMARK 500 O HOH B 132 O HOH B 153 2.06 REMARK 500 O HOH B 133 O HOH B 161 2.07 REMARK 500 O HOH B 133 O HOH A 267 2.09 REMARK 500 O HOH A 258 O HOH A 267 2.10 REMARK 500 O HOH B 137 O HOH B 141 2.14 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 017 A 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 103 DBREF 6OPT B 1 99 UNP Q7ZCI0 Q7ZCI0_9HIV1 1 99 DBREF 6OPT A 1 99 UNP Q7ZCI0 Q7ZCI0_9HIV1 1 99 SEQADV 6OPT LYS B 7 UNP Q7ZCI0 GLN 7 ENGINEERED MUTATION SEQADV 6OPT PHE B 82 UNP Q7ZCI0 VAL 82 ENGINEERED MUTATION SEQADV 6OPT LYS A 7 UNP Q7ZCI0 GLN 7 ENGINEERED MUTATION SEQADV 6OPT PHE A 82 UNP Q7ZCI0 VAL 82 ENGINEERED MUTATION 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 ASP THR VAL LEU GLU GLU MET ASN 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 CYS GLY HIS LYS ALA ILE GLY THR VAL LEU VAL GLY SEQRES 7 B 99 PRO THR PRO PHE ASN VAL ILE GLY ARG ASN LEU LEU THR SEQRES 8 B 99 GLN ILE GLY CYS THR LEU ASN PHE 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 ASP THR VAL LEU GLU GLU MET ASN 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 CYS GLY HIS LYS ALA ILE GLY THR VAL LEU VAL GLY SEQRES 7 A 99 PRO THR PRO PHE ASN VAL ILE GLY ARG ASN LEU LEU THR SEQRES 8 A 99 GLN ILE GLY CYS THR LEU ASN PHE HET 017 A 101 75 HET SO4 A 102 5 HET SO4 A 103 5 HETNAM 017 (3R,3AS,6AR)-HEXAHYDROFURO[2,3-B]FURAN-3-YL(1S,2R)-3- HETNAM 2 017 [[(4-AMINOPHENYL)SULFONYL](ISOBUTYL)AMINO]-1-BENZYL-2- HETNAM 3 017 HYDROXYPROPYLCARBAMATE HETNAM SO4 SULFATE ION HETSYN 017 DARUNAVIR; TMC114; UIC-94017 FORMUL 3 017 C27 H37 N3 O7 S FORMUL 4 SO4 2(O4 S 2-) FORMUL 6 HOH *142(H2 O) HELIX 1 AA1 GLY B 86 THR B 91 1 6 HELIX 2 AA2 GLN B 92 GLY B 94 5 3 HELIX 3 AA3 GLY A 86 THR A 91 1 6 SHEET 1 AA1 4 GLN B 2 THR B 4 0 SHEET 2 AA1 4 THR A 96 ASN A 98 -1 O LEU A 97 N ILE B 3 SHEET 3 AA1 4 THR B 96 ASN B 98 -1 N THR B 96 O ASN A 98 SHEET 4 AA1 4 GLN A 2 ILE A 3 -1 O ILE A 3 N LEU B 97 SHEET 1 AA2 8 LYS B 43 GLY B 49 0 SHEET 2 AA2 8 GLY B 52 ILE B 66 -1 O VAL B 56 N LYS B 45 SHEET 3 AA2 8 HIS B 69 GLY B 78 -1 O ALA B 71 N ILE B 64 SHEET 4 AA2 8 THR B 31 GLU B 34 1 N LEU B 33 O LEU B 76 SHEET 5 AA2 8 VAL B 84 ILE B 85 -1 O VAL B 84 N VAL B 32 SHEET 6 AA2 8 GLN B 18 LEU B 24 1 N LEU B 23 O ILE B 85 SHEET 7 AA2 8 LEU B 10 ILE B 15 -1 N ILE B 13 O LYS B 20 SHEET 8 AA2 8 GLY B 52 ILE B 66 -1 O GLU B 65 N LYS B 14 SHEET 1 AA3 8 LYS A 43 GLY A 49 0 SHEET 2 AA3 8 GLY A 52 ILE A 66 -1 O GLY A 52 N GLY A 49 SHEET 3 AA3 8 HIS A 69 VAL A 77 -1 O HIS A 69 N ILE A 66 SHEET 4 AA3 8 VAL A 32 LEU A 33 1 N LEU A 33 O LEU A 76 SHEET 5 AA3 8 VAL A 84 ILE A 85 -1 O VAL A 84 N VAL A 32 SHEET 6 AA3 8 GLN A 18 LEU A 24 1 N LEU A 23 O ILE A 85 SHEET 7 AA3 8 LEU A 10 ILE A 15 -1 N ILE A 13 O LYS A 20 SHEET 8 AA3 8 GLY A 52 ILE A 66 -1 O GLU A 65 N LYS A 14 SITE 1 AC1 18 ASP A 25 GLY A 27 ALA A 28 ASP A 29 SITE 2 AC1 18 ASP A 30 GLY A 48 ILE A 50 HOH A 213 SITE 3 AC1 18 HOH A 220 ASP B 25 GLY B 27 ALA B 28 SITE 4 AC1 18 ASP B 30 VAL B 32 GLY B 48 GLY B 49 SITE 5 AC1 18 PRO B 81 PHE B 82 SITE 1 AC2 6 GLY A 68 HIS A 69 LYS A 70 HOH A 203 SITE 2 AC2 6 HOH A 222 PRO B 1 SITE 1 AC3 5 MET A 36 ASN A 37 HOH A 243 PRO B 39 SITE 2 AC3 5 GLY B 40 CRYST1 50.774 57.852 61.543 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 0.019695 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017285 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016249 0.00000