HEADER HYDROLASE 17-JUL-19 6PU8 TITLE ROOM TEMPERATURE X-RAY STRUCTURE OF HIV-1 PROTEASE TRIPLE MUTANT TITLE 2 (V32I,I47V,V82I) WITH TETRAHEDRAL INTERMEDIATE OF KETO-DARUNAVIR COMPND MOL_ID: 1; COMPND 2 MOLECULE: HIV-1 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 HIV-1 PROTEASE, ASPARTIC PROTEASE, TETRAHEDRAL INTERMEDIATE KEYWDS 2 INHIBITOR, HOMODIMER, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR A.KOVALEVSKY,A.DAS REVDAT 2 11-OCT-23 6PU8 1 REMARK REVDAT 1 24-JUN-20 6PU8 0 JRNL AUTH M.KUMAR,K.MANDAL,M.P.BLAKELEY,T.WYMORE,S.B.H.KENT,J.M.LOUIS, JRNL AUTH 2 A.DAS,A.KOVALEVSKY JRNL TITL VISUALIZING TETRAHEDRAL OXYANION BOUND IN HIV-1 PROTEASE JRNL TITL 2 USING NEUTRONS: IMPLICATIONS FOR THE CATALYTIC MECHANISM AND JRNL TITL 3 DRUG DESIGN. JRNL REF ACS OMEGA V. 5 11605 2020 JRNL REFN ESSN 2470-1343 JRNL PMID 32478251 JRNL DOI 10.1021/ACSOMEGA.0C00835 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL-97 REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 92.2 REMARK 3 CROSS-VALIDATION METHOD : FREE R-VALUE REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.190 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.186 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.241 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 1074 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 21338 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.175 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.171 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.225 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 919 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 18314 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1514 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 39 REMARK 3 SOLVENT ATOMS : 121 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 1658.5 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 0.00 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 0 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 6699 REMARK 3 NUMBER OF RESTRAINTS : 6296 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.009 REMARK 3 ANGLE DISTANCES (A) : 0.027 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.025 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.047 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.064 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.025 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.000 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.085 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.000 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: NULL REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH AND HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6PU8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 25-JUL-19. REMARK 100 THE DEPOSITION ID IS D_1000243086. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-NOV-16 REMARK 200 TEMPERATURE (KELVIN) : 293 REMARK 200 PH : 6.0 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 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5406 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV++ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 22743 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 200 DATA REDUNDANCY : 3.900 REMARK 200 R MERGE (I) : 0.03700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 29.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.86 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.80 REMARK 200 R MERGE FOR SHELL (I) : 0.48100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.200 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: 5E5J REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.28 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.81 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M MES, 1.0 M NACL, PH 6.0, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 293K 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 29.81550 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 43.71900 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 29.81550 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 43.71900 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: 4030 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9550 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -22.0 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: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 87 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES 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 P3V B 201 DBREF 6PU8 A 1 99 UNP Q7SSI0 Q7SSI0_9HIV1 1 99 DBREF 6PU8 B 101 199 UNP Q7SSI0 Q7SSI0_9HIV1 1 99 SEQADV 6PU8 LYS A 7 UNP Q7SSI0 GLN 7 ENGINEERED MUTATION SEQADV 6PU8 ILE A 32 UNP Q7SSI0 VAL 32 ENGINEERED MUTATION SEQADV 6PU8 ILE A 33 UNP Q7SSI0 LEU 33 ENGINEERED MUTATION SEQADV 6PU8 VAL A 47 UNP Q7SSI0 ILE 47 ENGINEERED MUTATION SEQADV 6PU8 ILE A 63 UNP Q7SSI0 LEU 63 ENGINEERED MUTATION SEQADV 6PU8 ALA A 67 UNP Q7SSI0 CYS 67 ENGINEERED MUTATION SEQADV 6PU8 ILE A 82 UNP Q7SSI0 VAL 82 ENGINEERED MUTATION SEQADV 6PU8 ALA A 95 UNP Q7SSI0 SER 95 ENGINEERED MUTATION SEQADV 6PU8 LYS B 107 UNP Q7SSI0 GLN 7 ENGINEERED MUTATION SEQADV 6PU8 ILE B 132 UNP Q7SSI0 VAL 32 ENGINEERED MUTATION SEQADV 6PU8 ILE B 133 UNP Q7SSI0 LEU 33 ENGINEERED MUTATION SEQADV 6PU8 VAL B 147 UNP Q7SSI0 ILE 47 ENGINEERED MUTATION SEQADV 6PU8 ILE B 163 UNP Q7SSI0 LEU 63 ENGINEERED MUTATION SEQADV 6PU8 ALA B 167 UNP Q7SSI0 CYS 67 ENGINEERED MUTATION SEQADV 6PU8 ILE B 182 UNP Q7SSI0 VAL 82 ENGINEERED MUTATION SEQADV 6PU8 ALA B 195 UNP Q7SSI0 SER 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 ASP THR ILE ILE GLU GLU MET SER LEU PRO SEQRES 4 A 99 GLY ARG TRP LYS PRO LYS MET VAL 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 ILE 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 ASP THR ILE ILE GLU GLU MET SER LEU PRO SEQRES 4 B 99 GLY ARG TRP LYS PRO LYS MET VAL 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 ILE ASN ILE ILE GLY ARG ASN LEU LEU THR SEQRES 8 B 99 GLN ILE GLY ALA THR LEU ASN PHE HET P3V B 201 39 HETNAM P3V (3R,3AS,6AR)-HEXAHYDROFURO[2,3-B]FURAN-3-YL [(2S)-4- HETNAM 2 P3V {[(4-AMINOPHENYL)SULFONYL](2-METHYLPROPYL)AMINO}-3,3- HETNAM 3 P3V DIHYDROXY-1-PHENYLBUTAN-2-YL]CARBAMATE FORMUL 3 P3V C27 H37 N3 O8 S FORMUL 4 HOH *121(H2 O) HELIX 1 AA1 GLY A 86 THR A 91 1 6 HELIX 2 AA2 GLN A 92 GLY A 94 5 3 HELIX 3 AA3 GLY B 186 THR B 191 1 6 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 THR A 96 O ASN B 198 SHEET 4 AA1 4 GLN B 102 ILE B 103 -1 O ILE B 103 N LEU A 97 SHEET 1 AA2 8 LYS A 43 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 ILE 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 143 GLY B 149 0 SHEET 2 AA3 8 GLY B 152 ILE B 166 -1 O ILE B 154 N VAL B 147 SHEET 3 AA3 8 HIS B 169 VAL B 177 -1 O HIS B 169 N ILE B 166 SHEET 4 AA3 8 ILE 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 ILE 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 SITE 1 AC1 17 ASP A 25 GLY A 27 ALA A 28 ASP A 30 SITE 2 AC1 17 ILE A 32 VAL A 47 GLY A 48 GLY A 49 SITE 3 AC1 17 ILE A 82 ASP B 125 GLY B 127 ASP B 129 SITE 4 AC1 17 ASP B 130 GLY B 148 ILE B 150 ILE B 182 SITE 5 AC1 17 HOH B 318 CRYST1 59.631 87.438 46.429 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 0.016770 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011437 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021538 0.00000