HEADER HYDROLASE, VIRAL PROTEIN 01-MAR-19 6O57 TITLE CRYSTAL STRUCTURE OF MULTI-DRUG RESISTANT HIV-1 PROTEASE PR-S17 WITH A TITLE 2 SUBSTRATE ANALOG P2-NC IN P41 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 BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS HIV PROTEASE, HYDROLASE, VIRAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR Y.-F.WANG,J.AGNISWAMY,I.T.WEBER REVDAT 4 11-OCT-23 6O57 1 REMARK REVDAT 3 18-DEC-19 6O57 1 REMARK REVDAT 2 17-JUL-19 6O57 1 REMARK REVDAT 1 19-JUN-19 6O57 0 JRNL AUTH J.AGNISWAMY,D.W.KNELLER,R.BROTHERS,Y.F.WANG,R.W.HARRISON, JRNL AUTH 2 I.T.WEBER JRNL TITL HIGHLY DRUG-RESISTANT HIV-1 PROTEASE MUTANT PRS17 SHOWS JRNL TITL 2 ENHANCED BINDING TO SUBSTRATE ANALOGUES. JRNL REF ACS OMEGA V. 4 8707 2019 JRNL REFN ESSN 2470-1343 JRNL PMID 31172041 JRNL DOI 10.1021/ACSOMEGA.9B00683 REMARK 2 REMARK 2 RESOLUTION. 1.71 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0222 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.71 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.46 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 24824 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : FREE R-VALUE REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.200 REMARK 3 R VALUE (WORKING SET) : 0.198 REMARK 3 FREE R VALUE : 0.231 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 1262 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.71 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.75 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1732 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 93.30 REMARK 3 BIN R VALUE (WORKING SET) : 0.2860 REMARK 3 BIN FREE R VALUE SET COUNT : 79 REMARK 3 BIN FREE R VALUE : 0.3160 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1522 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 66 REMARK 3 SOLVENT ATOMS : 78 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 37.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 40.74 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.71000 REMARK 3 B22 (A**2) : 0.71000 REMARK 3 B33 (A**2) : -1.41000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.108 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.107 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.082 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.711 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.966 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.956 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1702 ; 0.021 ; 0.014 REMARK 3 BOND LENGTHS OTHERS (A): 1664 ; 0.001 ; 0.017 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2327 ; 2.206 ; 1.699 REMARK 3 BOND ANGLES OTHERS (DEGREES): 3897 ; 1.171 ; 1.680 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 221 ; 7.924 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 72 ;37.418 ;22.778 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 294 ;14.326 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 10 ; 9.790 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 240 ; 0.141 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1922 ; 0.013 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 300 ; 0.005 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 842 ; 3.124 ; 3.318 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 843 ; 3.122 ; 3.317 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1059 ; 4.100 ; 4.951 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1060 ; 4.098 ; 4.950 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 860 ; 3.966 ; 3.702 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 853 ; 3.978 ; 3.710 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 1263 ; 5.870 ; 5.383 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 1664 ; 6.822 ;37.867 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 1656 ; 6.805 ;37.794 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 1 A 99 REMARK 3 ORIGIN FOR THE GROUP (A): 72.6906 12.1597 18.4754 REMARK 3 T TENSOR REMARK 3 T11: 0.0131 T22: 0.0807 REMARK 3 T33: 0.0648 T12: 0.0180 REMARK 3 T13: -0.0175 T23: -0.0068 REMARK 3 L TENSOR REMARK 3 L11: 0.4255 L22: 0.1551 REMARK 3 L33: 1.0816 L12: 0.0537 REMARK 3 L13: -0.1006 L23: -0.4082 REMARK 3 S TENSOR REMARK 3 S11: -0.0501 S12: -0.1676 S13: -0.0110 REMARK 3 S21: 0.0138 S22: -0.0501 S23: -0.0333 REMARK 3 S31: -0.0447 S32: 0.1106 S33: 0.1003 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 1 B 99 REMARK 3 ORIGIN FOR THE GROUP (A): 70.1716 9.6760 -3.3351 REMARK 3 T TENSOR REMARK 3 T11: 0.0791 T22: 0.0161 REMARK 3 T33: 0.0650 T12: 0.0199 REMARK 3 T13: -0.0070 T23: -0.0186 REMARK 3 L TENSOR REMARK 3 L11: 0.1444 L22: 0.4284 REMARK 3 L33: 1.0125 L12: 0.1063 REMARK 3 L13: -0.3782 L23: -0.2018 REMARK 3 S TENSOR REMARK 3 S11: -0.0537 S12: 0.0106 S13: -0.0322 REMARK 3 S21: -0.1738 S22: -0.0492 S23: -0.0171 REMARK 3 S31: 0.1074 S32: -0.0454 S33: 0.1029 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 201 B 201 REMARK 3 ORIGIN FOR THE GROUP (A): 67.3836 13.9864 7.9264 REMARK 3 T TENSOR REMARK 3 T11: 0.0817 T22: 0.0883 REMARK 3 T33: 0.1171 T12: 0.0367 REMARK 3 T13: -0.0081 T23: 0.0207 REMARK 3 L TENSOR REMARK 3 L11: 5.9449 L22: 5.5865 REMARK 3 L33: 1.9799 L12: 4.0951 REMARK 3 L13: 3.4120 L23: 2.1330 REMARK 3 S TENSOR REMARK 3 S11: 0.0473 S12: 0.0484 S13: -0.0100 REMARK 3 S21: -0.0278 S22: -0.0748 S23: -0.1020 REMARK 3 S31: 0.0299 S32: 0.0458 S33: 0.0275 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 4 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 101 A 101 REMARK 3 RESIDUE RANGE : B 202 B 204 REMARK 3 RESIDUE RANGE : A 201 A 239 REMARK 3 RESIDUE RANGE : B 301 B 339 REMARK 3 ORIGIN FOR THE GROUP (A): 70.8673 13.0696 8.3152 REMARK 3 T TENSOR REMARK 3 T11: 0.0360 T22: 0.0649 REMARK 3 T33: 0.1243 T12: -0.0069 REMARK 3 T13: -0.0018 T23: -0.0142 REMARK 3 L TENSOR REMARK 3 L11: 0.7086 L22: 0.6748 REMARK 3 L33: 1.5110 L12: 0.0381 REMARK 3 L13: 0.5255 L23: -0.0036 REMARK 3 S TENSOR REMARK 3 S11: -0.0024 S12: 0.0268 S13: 0.0492 REMARK 3 S21: -0.0739 S22: -0.1212 S23: 0.0201 REMARK 3 S31: -0.0966 S32: -0.0364 S33: 0.1236 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: INITIALLY REFINED BY SHELX-2014 BUT REMARK 3 MOVED TO REFMAC DURING LATER CYCLES OF REFINEMENT. REMARK 4 REMARK 4 6O57 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-MAR-19. REMARK 100 THE DEPOSITION ID IS D_1000240042. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-FEB-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.6 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 MX300-HS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 26117 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.710 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 200 DATA REDUNDANCY : 6.100 REMARK 200 R MERGE (I) : 0.07100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 21.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.71 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.77 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.2 REMARK 200 DATA REDUNDANCY IN SHELL : 3.40 REMARK 200 R MERGE FOR SHELL (I) : 0.47100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.600 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: 1SGU REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.07 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.87 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 29.5% PEG 4000, 0.2M AMMONIUM ACETATE REMARK 280 AND 0.1M SODIUM ACETATE BUFFER AT PH 4.6, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y,X,Z+1/4 REMARK 290 4555 Y,-X,Z+3/4 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 41.06550 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 20.53275 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 61.59825 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: 4740 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9750 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -23.0 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 LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 THR B 80 N THR B 80 CA -0.133 REMARK 500 REMARK 500 REMARK: NULL 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 - NH2 ANGL. DEV. = -3.5 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ALA A 67 69.37 -154.52 REMARK 500 ASP B 35 40.28 -98.87 REMARK 500 ALA B 67 -53.50 -137.43 REMARK 500 ALA B 67 -101.28 27.75 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 ILE B 66 ALA B 67 -142.96 REMARK 500 REMARK 500 REMARK: NULL REMARK 630 REMARK 630 MOLECULE TYPE: PEPTIDE-LIKE INHIBITOR REMARK 630 MOLECULE NAME: N-{(2S)-2-[(N-ACETYL-L-THREONYL-L-ISOLEUCYL)AMINO] REMARK 630 HEXYL}-L-NORLEUCYL-L-GLUTAMINYL-N~5~-[AMINO(IMINIO)METHYL]-L- REMARK 630 ORNITHINAMIDE REMARK 630 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 630 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 630 REMARK 630 M RES C SSSEQI REMARK 630 2NC B 201 REMARK 630 SOURCE: NULL REMARK 630 TAXONOMY: NULL REMARK 630 SUBCOMP: ACE THR ILE 2A0 GLN ARG NH2 REMARK 630 DETAILS: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue FMT A 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 2NC B 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue FMT B 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue FMT B 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue FMT B 204 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2AOD RELATED DB: PDB REMARK 900 WILD TYPE HIV-1 PROTEASE WITH A SUBSTRATE ANALOG P2-NC REMARK 900 RELATED ID: 6O48 RELATED DB: PDB REMARK 900 WILD TYPE HIV-1 PROTEASE WITH A SUBSTRATE ANALOG CA-P2 REMARK 900 RELATED ID: 6O54 RELATED DB: PDB REMARK 900 MULTI-DRUG RESISTANT HIV-1 PROTEASE PR-S17 (D25N) REMARK 900 RELATED ID: 5T2E RELATED DB: PDB REMARK 900 MULTI-DRUG RESISTANT HIV-1 PROTEASE PR-S17 REMARK 900 RELATED ID: 6O5X RELATED DB: PDB REMARK 900 MULTI-DRUG RESISTANT HIV-1 PROTEASE PR-S17 WITH CA/P2 DBREF 6O57 A 1 99 UNP I7BFC3 I7BFC3_9HIV1 1 99 DBREF 6O57 B 1 99 UNP I7BFC3 I7BFC3_9HIV1 1 99 SEQADV 6O57 LEU A 46 UNP I7BFC3 MET 46 ENGINEERED MUTATION SEQADV 6O57 VAL A 48 UNP I7BFC3 GLY 48 ENGINEERED MUTATION SEQADV 6O57 ALA A 67 UNP I7BFC3 CYS 67 ENGINEERED MUTATION SEQADV 6O57 ILE A 77 UNP I7BFC3 VAL 77 ENGINEERED MUTATION SEQADV 6O57 SER A 82 UNP I7BFC3 ALA 82 ENGINEERED MUTATION SEQADV 6O57 LEU A 93 UNP I7BFC3 ILE 93 ENGINEERED MUTATION SEQADV 6O57 ALA A 95 UNP I7BFC3 CYS 95 ENGINEERED MUTATION SEQADV 6O57 LEU B 46 UNP I7BFC3 MET 46 ENGINEERED MUTATION SEQADV 6O57 VAL B 48 UNP I7BFC3 GLY 48 ENGINEERED MUTATION SEQADV 6O57 ALA B 67 UNP I7BFC3 CYS 67 ENGINEERED MUTATION SEQADV 6O57 ILE B 77 UNP I7BFC3 VAL 77 ENGINEERED MUTATION SEQADV 6O57 SER B 82 UNP I7BFC3 ALA 82 ENGINEERED MUTATION SEQADV 6O57 LEU B 93 UNP I7BFC3 ILE 93 ENGINEERED MUTATION SEQADV 6O57 ALA B 95 UNP I7BFC3 CYS 95 ENGINEERED MUTATION SEQRES 1 A 99 PRO GLN ILE THR LEU TRP GLN ARG PRO ILE VAL THR ILE SEQRES 2 A 99 LYS ILE GLY GLY GLN LEU ARG GLU ALA LEU LEU ASP THR SEQRES 3 A 99 GLY ALA ASP ASP THR VAL LEU GLU ASP ILE ASP LEU PRO SEQRES 4 A 99 GLY ARG TRP LYS PRO LYS LEU ILE VAL GLY ILE GLY GLY SEQRES 5 A 99 PHE VAL LYS VAL ARG GLN TYR GLU GLN VAL PRO ILE GLU SEQRES 6 A 99 ILE ALA GLY HIS LYS VAL VAL GLY THR VAL LEU ILE GLY SEQRES 7 A 99 PRO THR PRO SER ASN ILE ILE GLY ARG ASN LEU MET THR SEQRES 8 A 99 GLN LEU GLY ALA THR LEU ASN PHE SEQRES 1 B 99 PRO GLN ILE THR LEU TRP GLN ARG PRO ILE VAL THR ILE SEQRES 2 B 99 LYS ILE GLY GLY GLN LEU ARG GLU ALA LEU LEU ASP THR SEQRES 3 B 99 GLY ALA ASP ASP THR VAL LEU GLU ASP ILE ASP LEU PRO SEQRES 4 B 99 GLY ARG TRP LYS PRO LYS LEU ILE VAL GLY ILE GLY GLY SEQRES 5 B 99 PHE VAL LYS VAL ARG GLN TYR GLU GLN VAL PRO ILE GLU SEQRES 6 B 99 ILE ALA GLY HIS LYS VAL VAL GLY THR VAL LEU ILE GLY SEQRES 7 B 99 PRO THR PRO SER ASN ILE ILE GLY ARG ASN LEU MET THR SEQRES 8 B 99 GLN LEU GLY ALA THR LEU ASN PHE HET FMT A 101 3 HET 2NC B 201 54 HET FMT B 202 3 HET FMT B 203 3 HET FMT B 204 3 HETNAM FMT FORMIC ACID HETNAM 2NC N-{(2S)-2-[(N-ACETYL-L-THREONYL-L-ISOLEUCYL) HETNAM 2 2NC AMINO]HEXYL}-L-NORLEUCYL-L-GLUTAMINYL-N~5~- HETNAM 3 2NC [AMINO(IMINIO)METHYL]-L-ORNITHINAMIDE HETSYN 2NC P2/NC FORMUL 3 FMT 4(C H2 O2) FORMUL 4 2NC C35 H68 N11 O8 1+ FORMUL 8 HOH *78(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 THR A 4 0 SHEET 2 AA1 4 THR B 96 ASN B 98 -1 O LEU B 97 N ILE A 3 SHEET 3 AA1 4 THR A 96 ASN A 98 -1 N ASN A 98 O THR B 96 SHEET 4 AA1 4 GLN B 2 THR B 4 -1 O ILE B 3 N LEU A 97 SHEET 1 AA2 8 LYS A 43 GLY A 49 0 SHEET 2 AA2 8 GLY A 52 GLU A 65 -1 O GLN A 58 N LYS A 43 SHEET 3 AA2 8 LYS A 70 ILE A 77 -1 O VAL A 71 N ILE A 64 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 ILE A 10 ILE A 15 -1 N ILE A 13 O ARG A 20 SHEET 8 AA2 8 GLY A 52 GLU A 65 -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 GLU B 65 -1 O GLN B 58 N LYS B 43 SHEET 3 AA3 8 LYS B 70 ILE B 77 -1 O ILE B 77 N ARG B 57 SHEET 4 AA3 8 VAL B 32 LEU B 33 1 N LEU B 33 O LEU B 76 SHEET 5 AA3 8 ILE B 84 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 ILE B 10 ILE B 15 -1 N ILE B 13 O ARG B 20 SHEET 8 AA3 8 GLY B 52 GLU B 65 -1 O GLU B 65 N LYS B 14 SITE 1 AC1 3 GLN A 2 ARG A 57 HOH A 228 SITE 1 AC2 29 ARG A 8 ASP A 25 GLY A 27 ALA A 28 SITE 2 AC2 29 ASP A 29 ASP A 30 ILE A 47 VAL A 48 SITE 3 AC2 29 GLY A 49 ILE A 50 THR A 80 PRO A 81 SITE 4 AC2 29 SER A 82 ILE A 84 HOH A 203 ARG B 8 SITE 5 AC2 29 ASP B 25 GLY B 27 ALA B 28 ASP B 29 SITE 6 AC2 29 ASP B 30 ILE B 47 VAL B 48 GLY B 49 SITE 7 AC2 29 ILE B 50 THR B 80 ILE B 84 HOH B 308 SITE 8 AC2 29 HOH B 323 SITE 1 AC3 3 GLU B 21 HOH B 322 HOH B 333 SITE 1 AC4 4 PRO A 81 VAL B 48 VAL B 72 GLN B 92 SITE 1 AC5 5 VAL A 72 GLN A 92 HOH A 239 PRO B 81 SITE 2 AC5 5 HOH B 305 CRYST1 54.881 54.881 82.131 90.00 90.00 90.00 P 41 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 0.018221 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018221 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012176 0.00000