HEADER HYDROLASE/HYDROLASE INHIBITOR 14-MAY-19 6OXO TITLE HIV-1 PROTEASE NL4-3 WT IN COMPLEX WITH LR2-91 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,L.N.RUSERE,S.K.LEE,M.HENES,K.KOSOVRASTI,E.SPIELVOGEL, AUTHOR 2 E.A.NALIVAIKA,R.SWANSTROM,N.KURTYILMAZ,C.A.SCHIFFER,A.ALI REVDAT 4 13-MAR-24 6OXO 1 REMARK REVDAT 3 01-JAN-20 6OXO 1 REMARK REVDAT 2 25-SEP-19 6OXO 1 JRNL REVDAT 1 21-AUG-19 6OXO 0 JRNL AUTH L.N.RUSERE,G.J.LOCKBAUM,S.K.LEE,M.HENES,K.KOSOVRASTI, JRNL AUTH 2 E.SPIELVOGEL,E.A.NALIVAIKA,R.SWANSTROM,N.K.YILMAZ, JRNL AUTH 3 C.A.SCHIFFER,A.ALI JRNL TITL HIV-1 PROTEASE INHIBITORS INCORPORATING STEREOCHEMICALLY JRNL TITL 2 DEFINED P2' LIGANDS TO OPTIMIZE HYDROGEN BONDING IN THE JRNL TITL 3 SUBSTRATE ENVELOPE. JRNL REF J.MED.CHEM. V. 62 8062 2019 JRNL REFN ISSN 0022-2623 JRNL PMID 31386368 JRNL DOI 10.1021/ACS.JMEDCHEM.9B00838 REMARK 2 REMARK 2 RESOLUTION. 2.00 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 23.40 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 12934 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.203 REMARK 3 R VALUE (WORKING SET) : 0.201 REMARK 3 FREE R VALUE : 0.250 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.020 REMARK 3 FREE R VALUE TEST SET COUNT : 649 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 23.4009 - 3.4225 0.99 2564 138 0.1821 0.2215 REMARK 3 2 3.4225 - 2.7179 1.00 2473 131 0.2078 0.2540 REMARK 3 3 2.7179 - 2.3747 1.00 2434 127 0.2333 0.2947 REMARK 3 4 2.3747 - 2.1577 1.00 2436 127 0.2187 0.2846 REMARK 3 5 2.1577 - 2.0032 0.98 2378 126 0.2031 0.2654 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) : 0.190 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.910 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 : 0.002 1598 REMARK 3 ANGLE : 0.547 2179 REMARK 3 CHIRALITY : 0.050 256 REMARK 3 PLANARITY : 0.002 265 REMARK 3 DIHEDRAL : 13.386 922 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 6OXO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-MAY-19. REMARK 100 THE DEPOSITION ID IS D_1000241540. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-DEC-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 : 13010 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 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 (%) : 99.7 REMARK 200 DATA REDUNDANCY : 6.700 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) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.16 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.54 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.14 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 22-26% (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 25.53800 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 31.08800 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 29.20600 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 31.08800 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 25.53800 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 29.20600 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: 4790 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9260 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -78.0 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 ASN B 37 CG OD1 ND2 REMARK 470 ARG B 41 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 55 CG CD CE NZ REMARK 470 LYS A 7 CG CD CE NZ REMARK 470 ARG A 41 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 70 CG CD CE NZ 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 B 232 O HOH B 259 2.11 REMARK 500 O HOH B 244 O HOH B 257 2.18 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 SO4 B 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 B 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NJM A 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 103 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 104 DBREF 6OXO B 1 99 UNP Q8ULI9 Q8ULI9_9HIV1 1 99 DBREF 6OXO A 1 99 UNP Q8ULI9 Q8ULI9_9HIV1 1 99 SEQADV 6OXO LYS B 7 UNP Q8ULI9 GLN 7 ENGINEERED MUTATION SEQADV 6OXO LYS A 7 UNP Q8ULI9 GLN 7 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 VAL ASN ILE 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 VAL ASN ILE ILE GLY ARG ASN LEU LEU THR SEQRES 8 A 99 GLN ILE GLY CYS THR LEU ASN PHE HET SO4 B 101 5 HET SO4 B 102 5 HET NJM A 101 77 HET SO4 A 102 5 HET SO4 A 103 5 HET SO4 A 104 5 HETNAM SO4 SULFATE ION HETNAM NJM (3R,3AS,6AR)-HEXAHYDROFURO[2,3-B]FURAN-3-YL {(2S,3R)-3- HETNAM 2 NJM HYDROXY-4-[{[4-(HYDROXYMETHYL)PHENYL]SULFONYL}(2- HETNAM 3 NJM METHYLPROPYL)AMINO]-1-PHENYLBUTAN-2-YL}CARBAMATE FORMUL 3 SO4 5(O4 S 2-) FORMUL 5 NJM C28 H38 N2 O8 S FORMUL 9 HOH *126(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 VAL B 77 -1 O ALA B 71 N ILE B 64 SHEET 4 AA2 8 THR B 31 LEU B 33 1 N LEU B 33 O LEU B 76 SHEET 5 AA2 8 ILE B 84 ILE B 85 -1 O ILE 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 48 0 SHEET 2 AA3 8 PHE A 53 ILE A 66 -1 O VAL A 56 N LYS A 45 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 ILE A 84 ILE A 85 -1 O ILE 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 PHE A 53 ILE A 66 -1 O GLU A 65 N LYS A 14 SITE 1 AC1 4 PRO A 39 GLY A 40 MET B 36 ASN B 37 SITE 1 AC2 5 LEU B 19 LYS B 20 GLU B 21 ASN B 83 SITE 2 AC2 5 HOH B 201 SITE 1 AC3 18 ASP A 25 GLY A 27 ALA A 28 ASP A 29 SITE 2 AC3 18 ASP A 30 GLY A 48 GLY A 49 ILE A 50 SITE 3 AC3 18 HOH A 203 ASP B 25 GLY B 27 ALA B 28 SITE 4 AC3 18 ASP B 29 ASP B 30 VAL B 32 GLY B 48 SITE 5 AC3 18 GLY B 49 PRO B 81 SITE 1 AC4 5 MET A 36 ASN A 37 HOH A 214 PRO B 39 SITE 2 AC4 5 GLY B 40 SITE 1 AC5 5 GLY A 68 HIS A 69 LYS A 70 HOH A 201 SITE 2 AC5 5 PRO B 1 SITE 1 AC6 3 LYS A 7 ARG A 8 HOH A 205 CRYST1 51.076 58.412 62.176 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 0.019579 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017120 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016083 0.00000