HEADER HYDROLASE/HYDROLASE INHIBITOR 26-NOV-14 4RVJ TITLE CRYSTAL STRUCTURE OF MULTIDRUG-RESISTANT CLINICAL ISOLATE A02 HIV-1 TITLE 2 PROTEASE IN COMPLEX WITH AMPRENAVIR COMPND MOL_ID: 1; COMPND 2 MOLECULE: HIV-1 PROTEASE; COMPND 3 CHAIN: A, B, C, D; COMPND 4 FRAGMENT: F95C; COMPND 5 ENGINEERED: 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-INHIBITOR COMPLEX, AMPRENAVIR, NON-PEPTIDIC PROTEASE KEYWDS 2 INHIBITOR, HYDROLASE, HYDROLASE-HYDROLASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR R.S.YEDIDI,H.GARIMELLA,J.D.KAUFMAN,D.DAS,P.T.WINGFIELD,H.MITSUYA REVDAT 2 28-FEB-24 4RVJ 1 REMARK SEQADV REVDAT 1 04-MAY-16 4RVJ 0 JRNL AUTH R.S.YEDIDI,K.MAEDA,M.AOKI,H.GARIMELLA,K.V.RAO,S.AKASAPU, JRNL AUTH 2 D.A.DAVIS,J.D.KAUFMAN,D.DAS,P.T.WINGFIELD,M.AMANO,A.K.GHOSH, JRNL AUTH 3 H.MITSUYA JRNL TITL ENHANCED ANTIVIRAL ACTIVITY BY THE P2-TRIS-TETRAHYDROFURAN JRNL TITL 2 MOIETY OF GRL-0519, A NOVEL NONPEPTIDIC HIV-1 PROTEASE JRNL TITL 3 INHIBITOR (PI), AGAINST MULTI-PI-RESISTANT AND HIGHLY JRNL TITL 4 DARUNAVIR-RESISTANT STRAINS OF HIV-1 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.7.3_928) 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.50 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.100 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 58771 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.172 REMARK 3 R VALUE (WORKING SET) : 0.171 REMARK 3 FREE R VALUE : 0.200 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.050 REMARK 3 FREE R VALUE TEST SET COUNT : 2967 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 27.4998 - 4.4085 1.00 2762 128 0.1557 0.1662 REMARK 3 2 4.4085 - 3.5014 1.00 2661 156 0.1441 0.1643 REMARK 3 3 3.5014 - 3.0595 1.00 2666 154 0.1635 0.1807 REMARK 3 4 3.0595 - 2.7801 1.00 2707 128 0.1778 0.2098 REMARK 3 5 2.7801 - 2.5810 1.00 2647 161 0.1831 0.2121 REMARK 3 6 2.5810 - 2.4289 1.00 2655 140 0.1732 0.2126 REMARK 3 7 2.4289 - 2.3073 1.00 2660 153 0.1690 0.1912 REMARK 3 8 2.3073 - 2.2069 1.00 2624 151 0.1596 0.2172 REMARK 3 9 2.2069 - 2.1220 1.00 2637 145 0.1622 0.1810 REMARK 3 10 2.1220 - 2.0488 1.00 2636 152 0.1668 0.1979 REMARK 3 11 2.0488 - 1.9847 1.00 2687 110 0.1724 0.2010 REMARK 3 12 1.9847 - 1.9280 1.00 2652 131 0.1654 0.2158 REMARK 3 13 1.9280 - 1.8773 1.00 2664 139 0.1665 0.2146 REMARK 3 14 1.8773 - 1.8315 1.00 2666 121 0.1823 0.1989 REMARK 3 15 1.8315 - 1.7899 1.00 2629 136 0.1801 0.2321 REMARK 3 16 1.7899 - 1.7518 1.00 2626 151 0.2009 0.2478 REMARK 3 17 1.7518 - 1.7167 1.00 2643 154 0.2036 0.2860 REMARK 3 18 1.7167 - 1.6844 1.00 2631 155 0.2138 0.2542 REMARK 3 19 1.6844 - 1.6543 1.00 2694 120 0.2313 0.2725 REMARK 3 20 1.6543 - 1.6262 1.00 2599 139 0.2452 0.2744 REMARK 3 21 1.6262 - 1.6000 1.00 2658 143 0.2673 0.3058 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 REMARK 3 SHRINKAGE RADIUS : 0.86 REMARK 3 K_SOL : 0.41 REMARK 3 B_SOL : 47.32 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.210 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.960 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) : 0.33370 REMARK 3 B22 (A**2) : -0.14260 REMARK 3 B33 (A**2) : -0.19110 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.15680 REMARK 3 B23 (A**2) : 0.00000 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 : 0.019 3174 REMARK 3 ANGLE : 1.987 4310 REMARK 3 CHIRALITY : 0.134 502 REMARK 3 PLANARITY : 0.009 540 REMARK 3 DIHEDRAL : 14.887 1230 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): -3.6453 13.0530 21.7283 REMARK 3 T TENSOR REMARK 3 T11: 0.0685 T22: 0.0735 REMARK 3 T33: 0.0810 T12: 0.0000 REMARK 3 T13: 0.0003 T23: -0.0144 REMARK 3 L TENSOR REMARK 3 L11: 0.1271 L22: 0.1010 REMARK 3 L33: 0.2559 L12: 0.0010 REMARK 3 L13: -0.0026 L23: -0.0354 REMARK 3 S TENSOR REMARK 3 S11: -0.0138 S12: 0.0001 S13: -0.0008 REMARK 3 S21: -0.0012 S22: 0.0056 S23: 0.0050 REMARK 3 S31: -0.0007 S32: -0.0595 S33: -0.0391 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 4RVJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-DEC-14. REMARK 100 THE DEPOSITION ID IS D_1000087847. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-MAR-12 REMARK 200 TEMPERATURE (KELVIN) : 100 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 : 21-ID-F REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.98 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX-225 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 65689 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.540 REMARK 200 RESOLUTION RANGE LOW (A) : 28.970 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 4.200 REMARK 200 R MERGE (I) : 0.10700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL 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: MOLREP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.56 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.59 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.6 M AMMONIUM SULFATE + 0.1 M CITRIC REMARK 280 ACID, PH 5.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 28.65500 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: 4840 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9490 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 350 REMARK 350 BIOMOLECULE: 2 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: 4820 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9590 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -22.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D 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 NE ARG C 45 O HOH C 129 1.81 REMARK 500 O HOH B 251 O HOH B 334 1.82 REMARK 500 O HOH C 131 O HOH C 216 1.89 REMARK 500 O HOH D 233 O HOH D 304 1.95 REMARK 500 NZ LYS C 70 O HOH C 162 1.96 REMARK 500 NH2 ARG C 8 O HOH C 187 1.99 REMARK 500 O HOH C 103 O HOH C 212 2.02 REMARK 500 NE2 GLN C 61 O HOH C 220 2.03 REMARK 500 OG1 THR D 82 O HOH D 292 2.03 REMARK 500 O HOH D 279 O HOH D 295 2.04 REMARK 500 OG1 THR B 82 O HOH B 300 2.04 REMARK 500 O HOH B 255 O HOH B 299 2.07 REMARK 500 OE2 GLU B 21 O HOH B 304 2.07 REMARK 500 O HOH B 273 O HOH B 327 2.08 REMARK 500 O HOH D 273 O HOH D 296 2.10 REMARK 500 CZ ARG C 8 O HOH C 187 2.14 REMARK 500 NH1 ARG C 45 O HOH C 147 2.15 REMARK 500 O HOH C 150 O HOH C 192 2.16 REMARK 500 O HOH B 314 O HOH B 326 2.17 REMARK 500 O HOH A 118 O HOH A 181 2.17 REMARK 500 NH1 ARG C 45 O HOH C 183 2.19 REMARK 500 O HOH C 161 O HOH D 246 2.19 REMARK 500 O HOH C 155 O HOH C 171 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 OE1 GLN B 61 O HOH A 112 2545 2.01 REMARK 500 OE1 GLN D 61 O HOH C 118 2556 2.05 REMARK 500 O HOH C 203 O HOH D 293 2546 2.13 REMARK 500 REMARK 500 REMARK: NULL 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 GLY A 51 CA GLY A 51 C 0.118 REMARK 500 CYS B 95 CB CYS B 95 SG -0.100 REMARK 500 GLY C 51 CA GLY C 51 C 0.112 REMARK 500 CYS D 95 CB CYS D 95 SG -0.102 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 GLY A 51 C - N - CA ANGL. DEV. = -22.8 DEGREES REMARK 500 GLY A 51 N - CA - C ANGL. DEV. = 19.1 DEGREES REMARK 500 ARG A 57 NE - CZ - NH2 ANGL. DEV. = -3.4 DEGREES REMARK 500 GLY C 51 C - N - CA ANGL. DEV. = -23.1 DEGREES REMARK 500 GLY C 51 N - CA - C ANGL. DEV. = 19.3 DEGREES REMARK 500 ARG C 57 NE - CZ - NH2 ANGL. DEV. = -3.0 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 PRO A 79 48.01 -82.89 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 GLY A 51 GLY A 52 -144.58 REMARK 500 GLY C 51 GLY C 52 -143.64 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 478 B 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 478 D 101 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4NJS RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF MULTIDRUG-RESISTANT CLINICAL ISOLATE A02 HIV-1 REMARK 900 PROTEASE IN COMPLEX WITH NON-PEPTIDIC INHIBITOR, GRL008 REMARK 900 RELATED ID: 4NJT RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF MULTIDRUG-RESISTANT CLINICAL ISOLATE A02 HIV-1 REMARK 900 PROTEASE IN COMPLEX WITH DARUNAVIR REMARK 900 RELATED ID: 4NJU RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF MULTIDRUG-RESISTANT CLINICAL ISOLATE A02 HIV-1 REMARK 900 PROTEASE IN COMPLEX WITH TIPRANAVIR REMARK 900 RELATED ID: 4NJV RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF MULTIDRUG-RESISTANT CLINICAL ISOLATE A02 HIV-1 REMARK 900 PROTEASE IN COMPLEX WITH RITONAVIR REMARK 900 RELATED ID: 4HLA RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF WILD TYPE HIV-1 PROTEASE IN COMPLEX WITH REMARK 900 DARUNAVIR REMARK 900 RELATED ID: 4RVI RELATED DB: PDB REMARK 900 RELATED ID: 4RVV RELATED DB: PDB REMARK 900 RELATED ID: 4RVX RELATED DB: PDB DBREF 4RVJ A 1 99 UNP Q9J006 Q9J006_9HIV1 1 99 DBREF 4RVJ B 1 99 UNP Q9J006 Q9J006_9HIV1 1 99 DBREF 4RVJ C 1 99 UNP Q9J006 Q9J006_9HIV1 1 99 DBREF 4RVJ D 1 99 UNP Q9J006 Q9J006_9HIV1 1 99 SEQADV 4RVJ CYS A 95 UNP Q9J006 PHE 95 ENGINEERED MUTATION SEQADV 4RVJ CYS B 95 UNP Q9J006 PHE 95 ENGINEERED MUTATION SEQADV 4RVJ CYS C 95 UNP Q9J006 PHE 95 ENGINEERED MUTATION SEQADV 4RVJ CYS D 95 UNP Q9J006 PHE 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 VAL GLY GLY GLN LEU LYS GLU ALA LEU LEU ASP THR SEQRES 3 A 99 GLY ALA ASP ASP THR VAL LEU GLU ASP MET GLU LEU PRO SEQRES 4 A 99 GLY ARG TRP LYS PRO ARG MET ILE GLY GLY ILE GLY GLY SEQRES 5 A 99 PHE VAL LYS VAL ARG GLN TYR ASP GLN ILE PRO ILE GLU SEQRES 6 A 99 ILE CYS GLY HIS LYS VAL ILE GLY THR VAL LEU VAL GLY SEQRES 7 A 99 PRO THR PRO THR ASN ILE ILE GLY ARG ASN LEU MET THR SEQRES 8 A 99 GLN LEU GLY CYS 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 VAL GLY GLY GLN LEU LYS GLU ALA LEU LEU ASP THR SEQRES 3 B 99 GLY ALA ASP ASP THR VAL LEU GLU ASP MET GLU LEU PRO SEQRES 4 B 99 GLY ARG TRP LYS PRO ARG MET ILE GLY GLY ILE GLY GLY SEQRES 5 B 99 PHE VAL LYS VAL ARG GLN TYR ASP GLN ILE PRO ILE GLU SEQRES 6 B 99 ILE CYS GLY HIS LYS VAL ILE GLY THR VAL LEU VAL GLY SEQRES 7 B 99 PRO THR PRO THR ASN ILE ILE GLY ARG ASN LEU MET THR SEQRES 8 B 99 GLN LEU GLY CYS THR LEU ASN PHE SEQRES 1 C 99 PRO GLN ILE THR LEU TRP GLN ARG PRO ILE VAL THR ILE SEQRES 2 C 99 LYS VAL GLY GLY GLN LEU LYS GLU ALA LEU LEU ASP THR SEQRES 3 C 99 GLY ALA ASP ASP THR VAL LEU GLU ASP MET GLU LEU PRO SEQRES 4 C 99 GLY ARG TRP LYS PRO ARG MET ILE GLY GLY ILE GLY GLY SEQRES 5 C 99 PHE VAL LYS VAL ARG GLN TYR ASP GLN ILE PRO ILE GLU SEQRES 6 C 99 ILE CYS GLY HIS LYS VAL ILE GLY THR VAL LEU VAL GLY SEQRES 7 C 99 PRO THR PRO THR ASN ILE ILE GLY ARG ASN LEU MET THR SEQRES 8 C 99 GLN LEU GLY CYS THR LEU ASN PHE SEQRES 1 D 99 PRO GLN ILE THR LEU TRP GLN ARG PRO ILE VAL THR ILE SEQRES 2 D 99 LYS VAL GLY GLY GLN LEU LYS GLU ALA LEU LEU ASP THR SEQRES 3 D 99 GLY ALA ASP ASP THR VAL LEU GLU ASP MET GLU LEU PRO SEQRES 4 D 99 GLY ARG TRP LYS PRO ARG MET ILE GLY GLY ILE GLY GLY SEQRES 5 D 99 PHE VAL LYS VAL ARG GLN TYR ASP GLN ILE PRO ILE GLU SEQRES 6 D 99 ILE CYS GLY HIS LYS VAL ILE GLY THR VAL LEU VAL GLY SEQRES 7 D 99 PRO THR PRO THR ASN ILE ILE GLY ARG ASN LEU MET THR SEQRES 8 D 99 GLN LEU GLY CYS THR LEU ASN PHE HET 478 B 101 35 HET 478 D 101 35 HETNAM 478 {3-[(4-AMINO-BENZENESULFONYL)-ISOBUTYL-AMINO]-1-BENZYL- HETNAM 2 478 2-HYDROXY-PROPYL}-CARBAMIC ACID TETRAHYDRO-FURAN-3-YL HETNAM 3 478 ESTER HETSYN 478 AMPRENAVIR FORMUL 5 478 2(C25 H35 N3 O6 S) FORMUL 7 HOH *483(H2 O) HELIX 1 1 GLY A 86 THR A 91 1 6 HELIX 2 2 GLN A 92 GLY A 94 5 3 HELIX 3 3 GLY B 86 GLY B 94 1 9 HELIX 4 4 GLY C 86 THR C 91 1 6 HELIX 5 5 GLN C 92 GLY C 94 5 3 HELIX 6 6 GLY D 86 GLY D 94 1 9 SHEET 1 A 4 GLN A 2 ILE A 3 0 SHEET 2 A 4 THR B 96 ASN B 98 -1 O LEU B 97 N ILE A 3 SHEET 3 A 4 THR A 96 ASN A 98 -1 N ASN A 98 O THR B 96 SHEET 4 A 4 GLN B 2 ILE B 3 -1 O ILE B 3 N LEU A 97 SHEET 1 B 8 LYS A 43 GLY A 49 0 SHEET 2 B 8 GLY A 52 ILE A 66 -1 O GLN A 58 N LYS A 43 SHEET 3 B 8 HIS A 69 GLY A 78 -1 O VAL A 71 N ILE A 64 SHEET 4 B 8 THR A 31 GLU A 34 1 N LEU A 33 O LEU A 76 SHEET 5 B 8 ILE A 84 ILE A 85 -1 O ILE A 84 N VAL A 32 SHEET 6 B 8 GLN A 18 LEU A 24 1 N LEU A 23 O ILE A 85 SHEET 7 B 8 ILE A 10 VAL A 15 -1 N ILE A 13 O LYS A 20 SHEET 8 B 8 GLY A 52 ILE A 66 -1 O GLU A 65 N LYS A 14 SHEET 1 C 8 LYS B 43 GLY B 49 0 SHEET 2 C 8 GLY B 52 ILE B 66 -1 O VAL B 54 N ILE B 47 SHEET 3 C 8 HIS B 69 VAL B 77 -1 O VAL B 71 N ILE B 64 SHEET 4 C 8 VAL B 32 LEU B 33 1 N LEU B 33 O LEU B 76 SHEET 5 C 8 ILE B 84 ILE B 85 -1 O ILE B 84 N VAL B 32 SHEET 6 C 8 GLN B 18 LEU B 24 1 N LEU B 23 O ILE B 85 SHEET 7 C 8 ILE B 10 VAL B 15 -1 N ILE B 13 O LYS B 20 SHEET 8 C 8 GLY B 52 ILE B 66 -1 O GLU B 65 N LYS B 14 SHEET 1 D 4 GLN C 2 ILE C 3 0 SHEET 2 D 4 THR D 96 ASN D 98 -1 O LEU D 97 N ILE C 3 SHEET 3 D 4 THR C 96 ASN C 98 -1 N ASN C 98 O THR D 96 SHEET 4 D 4 GLN D 2 ILE D 3 -1 O ILE D 3 N LEU C 97 SHEET 1 E 8 LYS C 43 GLY C 49 0 SHEET 2 E 8 GLY C 52 ILE C 66 -1 O GLN C 58 N LYS C 43 SHEET 3 E 8 HIS C 69 GLY C 78 -1 O VAL C 71 N ILE C 64 SHEET 4 E 8 THR C 31 GLU C 34 1 N LEU C 33 O LEU C 76 SHEET 5 E 8 ILE C 84 ILE C 85 -1 O ILE C 84 N VAL C 32 SHEET 6 E 8 GLN C 18 LEU C 24 1 N LEU C 23 O ILE C 85 SHEET 7 E 8 ILE C 10 VAL C 15 -1 N ILE C 13 O LYS C 20 SHEET 8 E 8 GLY C 52 ILE C 66 -1 O GLU C 65 N LYS C 14 SHEET 1 F 8 LYS D 43 GLY D 49 0 SHEET 2 F 8 GLY D 52 ILE D 66 -1 O VAL D 56 N ARG D 45 SHEET 3 F 8 HIS D 69 VAL D 77 -1 O VAL D 71 N ILE D 64 SHEET 4 F 8 VAL D 32 LEU D 33 1 N LEU D 33 O LEU D 76 SHEET 5 F 8 ILE D 84 ILE D 85 -1 O ILE D 84 N VAL D 32 SHEET 6 F 8 GLN D 18 LEU D 24 1 N LEU D 23 O ILE D 85 SHEET 7 F 8 ILE D 10 VAL D 15 -1 N ILE D 13 O LYS D 20 SHEET 8 F 8 GLY D 52 ILE D 66 -1 O GLU D 65 N LYS D 14 SITE 1 AC1 20 ASP A 25 GLY A 27 ALA A 28 ASP A 30 SITE 2 AC1 20 GLY A 48 GLY A 49 PRO A 81 THR A 82 SITE 3 AC1 20 HOH A 150 ASP B 25 GLY B 27 ALA B 28 SITE 4 AC1 20 ASP B 29 ASP B 30 VAL B 32 GLY B 48 SITE 5 AC1 20 GLY B 49 ILE B 50 ILE B 84 HOH B 202 SITE 1 AC2 18 ASP C 25 GLY C 27 ALA C 28 ASP C 30 SITE 2 AC2 18 GLY C 48 GLY C 49 THR C 82 ASP D 25 SITE 3 AC2 18 GLY D 27 ALA D 28 ASP D 29 ASP D 30 SITE 4 AC2 18 VAL D 32 GLY D 48 GLY D 49 ILE D 50 SITE 5 AC2 18 ILE D 84 HOH D 201 CRYST1 45.250 57.310 86.900 90.00 90.01 90.00 P 1 21 1 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 0.022099 0.000000 0.000004 0.00000 SCALE2 0.000000 0.017449 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011507 0.00000