HEADER HYDROLASE 12-DEC-03 1RV7 TITLE CRYSTAL STRUCTURES OF A MULTIDRUG-RESISTANT HIV-1 PROTEASE REVEAL AN TITLE 2 EXPANDED ACTIVE SITE CAVITY COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEASE; COMPND 3 CHAIN: A, B; COMPND 4 EC: 3.4.23.16; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HUMAN IMMUNODEFICIENCY VIRUS 1; SOURCE 3 ORGANISM_TAXID: 11676; SOURCE 4 GENE: HIV-1; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PJFV769NOHIS KEYWDS HIV PROTEASE, AIDS, POLYPROTEIN, HYDROLASE, ASPARTYL PROTEASE, MULTI- KEYWDS 2 DRUG RESISTANCE, LOPINAVIR EXPDTA X-RAY DIFFRACTION AUTHOR B.C.LOGSDON,J.F.VICKREY,P.MARTIN,G.PROTEASA,J.I.KOEPKE,S.R.TERLECKY, AUTHOR 2 Z.WAWRZAK,M.A.WINTERS,T.C.MERIGAN,L.C.KOVARI REVDAT 4 14-FEB-24 1RV7 1 REMARK REVDAT 3 27-OCT-21 1RV7 1 REMARK SEQADV HETSYN REVDAT 2 24-FEB-09 1RV7 1 VERSN REVDAT 1 14-DEC-04 1RV7 0 JRNL AUTH B.C.LOGSDON,J.F.VICKREY,P.MARTIN,G.PROTEASA,J.I.KOEPKE, JRNL AUTH 2 S.R.TERLECKY,Z.WAWRZAK,M.A.WINTERS,T.C.MERIGAN,L.C.KOVARI JRNL TITL CRYSTAL STRUCTURES OF A MULTIDRUG-RESISTANT HUMAN JRNL TITL 2 IMMUNODEFICIENCY VIRUS TYPE 1 PROTEASE REVEAL AN EXPANDED JRNL TITL 3 ACTIVE-SITE CAVITY. JRNL REF J.VIROL. V. 78 3123 2004 JRNL REFN ISSN 0022-538X JRNL PMID 14990731 JRNL DOI 10.1128/JVI.78.6.3123-3132.2004 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH J.F.VICKREY,B.C.LOGSDON,G.PROTEASA,S.PALMER,M.A.WINTERS, REMARK 1 AUTH 2 T.C.MERIGAN,L.C.KOVARI REMARK 1 TITL HIV-1 PROTEASE VARIANTS FROM 100-FOLD DRUG RESISTANT REMARK 1 TITL 2 CLINICAL ISOLATES: EXPRESSION, PURIFICATION, AND REMARK 1 TITL 3 CRYSTALLIZATION. REMARK 1 REF PROTEIN EXPR.PURIF. V. 28 165 2003 REMARK 1 REFN ISSN 1046-5928 REMARK 1 DOI 10.1016/S1046-5928(02)00650-2 REMARK 2 REMARK 2 RESOLUTION. 2.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.1.24 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.4 REMARK 3 NUMBER OF REFLECTIONS : 5288 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.271 REMARK 3 R VALUE (WORKING SET) : 0.271 REMARK 3 FREE R VALUE : 0.350 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.600 REMARK 3 FREE R VALUE TEST SET COUNT : 253 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) : 2.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.77 REMARK 3 REFLECTION IN BIN (WORKING SET) : 377 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2140 REMARK 3 BIN FREE R VALUE SET COUNT : 14 REMARK 3 BIN FREE R VALUE : 0.4320 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1510 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 46 REMARK 3 SOLVENT ATOMS : 36 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 38.81 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.97000 REMARK 3 B22 (A**2) : 0.97000 REMARK 3 B33 (A**2) : -1.94000 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): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.480 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.427 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 21.368 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.928 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.828 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1587 ; 0.087 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 1535 ; 0.003 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2156 ; 4.885 ; 2.005 REMARK 3 BOND ANGLES OTHERS (DEGREES): 3575 ; 1.989 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 196 ;10.543 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 256 ; 0.327 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1712 ; 0.025 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 281 ; 0.016 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 412 ; 0.328 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 2027 ; 0.319 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): 1189 ; 0.153 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 50 ; 0.297 ; 0.200 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): 49 ; 0.351 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 104 ; 0.392 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 8 ; 0.542 ; 0.200 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): 978 ; 2.649 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1594 ; 4.157 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 609 ; 5.883 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 562 ; 7.959 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL 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 : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 1RV7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-DEC-03. REMARK 100 THE DEPOSITION ID IS D_1000021063. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-MAY-03 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.7 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 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5148 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : OSMIC MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : CRYSTALCLEAR (MSC/RIGAKU) REMARK 200 DATA SCALING SOFTWARE : D*TREK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 5316 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.700 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL 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: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.61 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.44 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: MES, SODIUM CHLORIDE, PH 6.7, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 295K 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 51.83800 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 25.91900 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 77.75700 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: 3960 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10410 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 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 115 O HOH A 122 1.91 REMARK 500 NE2 GLN A 58 OD1 ASP A 60 2.06 REMARK 500 OD1 ASP B 29 NH2 ARG B 87 2.17 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 O TRP B 42 O HOH A 118 3565 1.64 REMARK 500 NH1 ARG B 41 O HOH A 125 3565 2.16 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 PRO A 1 CB PRO A 1 CG 0.356 REMARK 500 PRO A 1 CG PRO A 1 CD 0.249 REMARK 500 PRO A 1 CA PRO A 1 C -0.170 REMARK 500 GLN A 2 CG GLN A 2 CD 0.167 REMARK 500 ILE A 3 CB ILE A 3 CG2 0.193 REMARK 500 TRP A 6 CE2 TRP A 6 CZ2 -0.141 REMARK 500 TRP A 6 CE3 TRP A 6 CZ3 -0.149 REMARK 500 GLN A 7 CG GLN A 7 CD 0.353 REMARK 500 GLN A 7 CD GLN A 7 NE2 0.210 REMARK 500 GLN A 7 C GLN A 7 O 0.117 REMARK 500 ARG A 8 C ARG A 8 O 0.215 REMARK 500 PRO A 9 CB PRO A 9 CG -0.318 REMARK 500 PRO A 9 C PRO A 9 O -0.160 REMARK 500 VAL A 11 N VAL A 11 CA -0.163 REMARK 500 VAL A 11 CB VAL A 11 CG1 0.170 REMARK 500 THR A 12 CB THR A 12 OG1 0.161 REMARK 500 ILE A 13 CB ILE A 13 CG2 -0.313 REMARK 500 ILE A 15 CA ILE A 15 CB -0.154 REMARK 500 GLN A 18 CG GLN A 18 CD 0.140 REMARK 500 LEU A 19 CG LEU A 19 CD1 -0.233 REMARK 500 GLU A 21 CD GLU A 21 OE1 0.207 REMARK 500 THR A 26 CA THR A 26 CB -0.219 REMARK 500 GLY A 27 CA GLY A 27 C 0.102 REMARK 500 ASP A 29 CB ASP A 29 CG -0.202 REMARK 500 ASP A 29 CG ASP A 29 OD2 0.211 REMARK 500 THR A 31 CA THR A 31 C -0.172 REMARK 500 VAL A 32 N VAL A 32 CA 0.121 REMARK 500 VAL A 32 CB VAL A 32 CG1 -0.128 REMARK 500 GLU A 34 CB GLU A 34 CG 0.319 REMARK 500 GLU A 34 CG GLU A 34 CD 0.238 REMARK 500 GLU A 34 CD GLU A 34 OE1 0.117 REMARK 500 GLU A 34 CD GLU A 34 OE2 0.138 REMARK 500 GLU A 35 CB GLU A 35 CG 0.266 REMARK 500 GLU A 35 CG GLU A 35 CD 0.187 REMARK 500 GLU A 35 CD GLU A 35 OE1 0.115 REMARK 500 GLU A 35 CD GLU A 35 OE2 0.135 REMARK 500 GLU A 35 C GLU A 35 O 0.288 REMARK 500 VAL A 36 N VAL A 36 CA 0.179 REMARK 500 VAL A 36 CB VAL A 36 CG1 -0.277 REMARK 500 ASN A 37 CG ASN A 37 OD1 0.160 REMARK 500 ASN A 37 CA ASN A 37 C -0.183 REMARK 500 TRP A 42 CA TRP A 42 CB -0.160 REMARK 500 TRP A 42 CB TRP A 42 CG -0.158 REMARK 500 LYS A 43 CD LYS A 43 CE 0.204 REMARK 500 PRO A 44 CA PRO A 44 C 0.143 REMARK 500 GLY A 49 N GLY A 49 CA 0.113 REMARK 500 GLY A 49 CA GLY A 49 C 0.097 REMARK 500 GLY A 49 C GLY A 49 O 0.140 REMARK 500 ILE A 50 C ILE A 50 O 0.231 REMARK 500 PHE A 53 CA PHE A 53 CB 0.168 REMARK 500 REMARK 500 THIS ENTRY HAS 170 BOND DEVIATIONS. 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 PRO A 1 CB - CG - CD ANGL. DEV. = -17.2 DEGREES REMARK 500 THR A 4 CA - CB - CG2 ANGL. DEV. = -8.5 DEGREES REMARK 500 ARG A 8 NE - CZ - NH1 ANGL. DEV. = 4.5 DEGREES REMARK 500 ARG A 8 NE - CZ - NH2 ANGL. DEV. = -6.3 DEGREES REMARK 500 PRO A 9 C - N - CA ANGL. DEV. = 11.2 DEGREES REMARK 500 LEU A 19 CB - CG - CD2 ANGL. DEV. = 10.6 DEGREES REMARK 500 GLU A 21 OE1 - CD - OE2 ANGL. DEV. = 8.1 DEGREES REMARK 500 GLU A 21 CG - CD - OE2 ANGL. DEV. = -17.1 DEGREES REMARK 500 ASP A 29 CB - CG - OD1 ANGL. DEV. = -11.6 DEGREES REMARK 500 LEU A 33 CB - CG - CD2 ANGL. DEV. = 10.3 DEGREES REMARK 500 GLU A 34 OE1 - CD - OE2 ANGL. DEV. = -7.9 DEGREES REMARK 500 ASN A 37 C - N - CA ANGL. DEV. = -15.1 DEGREES REMARK 500 ASN A 37 CB - CA - C ANGL. DEV. = -14.4 DEGREES REMARK 500 ARG A 41 NE - CZ - NH2 ANGL. DEV. = 3.4 DEGREES REMARK 500 TRP A 42 CD1 - NE1 - CE2 ANGL. DEV. = -6.0 DEGREES REMARK 500 LYS A 43 CD - CE - NZ ANGL. DEV. = 15.2 DEGREES REMARK 500 PHE A 53 N - CA - CB ANGL. DEV. = 11.0 DEGREES REMARK 500 PHE A 53 CA - C - O ANGL. DEV. = -13.0 DEGREES REMARK 500 ARG A 57 NE - CZ - NH2 ANGL. DEV. = 3.3 DEGREES REMARK 500 TYR A 59 CZ - CE2 - CD2 ANGL. DEV. = -8.0 DEGREES REMARK 500 ASP A 60 CB - CG - OD2 ANGL. DEV. = 6.2 DEGREES REMARK 500 VAL A 62 CB - CA - C ANGL. DEV. = -11.4 DEGREES REMARK 500 ILE A 64 CG1 - CB - CG2 ANGL. DEV. = -16.9 DEGREES REMARK 500 LEU A 76 CB - CG - CD1 ANGL. DEV. = -17.5 DEGREES REMARK 500 LEU A 76 CB - CG - CD2 ANGL. DEV. = 11.8 DEGREES REMARK 500 ALA A 82 N - CA - CB ANGL. DEV. = -8.5 DEGREES REMARK 500 ARG A 87 NE - CZ - NH2 ANGL. DEV. = -3.8 DEGREES REMARK 500 LEU A 89 CB - CG - CD2 ANGL. DEV. = 15.1 DEGREES REMARK 500 THR A 96 CA - CB - CG2 ANGL. DEV. = -11.3 DEGREES REMARK 500 ARG B 8 NE - CZ - NH2 ANGL. DEV. = -4.5 DEGREES REMARK 500 THR B 12 OG1 - CB - CG2 ANGL. DEV. = -15.3 DEGREES REMARK 500 LEU B 19 CB - CG - CD1 ANGL. DEV. = 16.4 DEGREES REMARK 500 LEU B 19 CB - CG - CD2 ANGL. DEV. = -10.9 DEGREES REMARK 500 GLU B 34 CG - CD - OE1 ANGL. DEV. = -12.8 DEGREES REMARK 500 GLU B 34 CG - CD - OE2 ANGL. DEV. = 14.5 DEGREES REMARK 500 GLU B 35 CG - CD - OE2 ANGL. DEV. = -13.5 DEGREES REMARK 500 ARG B 41 NH1 - CZ - NH2 ANGL. DEV. = -7.9 DEGREES REMARK 500 ARG B 41 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 ARG B 41 NE - CZ - NH2 ANGL. DEV. = 4.4 DEGREES REMARK 500 ILE B 47 CG1 - CB - CG2 ANGL. DEV. = -16.1 DEGREES REMARK 500 ARG B 57 NE - CZ - NH1 ANGL. DEV. = -3.9 DEGREES REMARK 500 TYR B 59 CZ - CE2 - CD2 ANGL. DEV. = -6.8 DEGREES REMARK 500 ASP B 60 CB - CG - OD2 ANGL. DEV. = 12.4 DEGREES REMARK 500 PRO B 63 N - CD - CG ANGL. DEV. = 10.4 DEGREES REMARK 500 GLU B 65 N - CA - CB ANGL. DEV. = -11.6 DEGREES REMARK 500 ILE B 66 CB - CA - C ANGL. DEV. = -12.2 DEGREES REMARK 500 VAL B 71 CG1 - CB - CG2 ANGL. DEV. = 17.7 DEGREES REMARK 500 GLY B 78 C - N - CA ANGL. DEV. = 12.8 DEGREES REMARK 500 PRO B 79 C - N - CA ANGL. DEV. = 11.7 DEGREES REMARK 500 PRO B 79 C - N - CD ANGL. DEV. = -15.2 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 52 ANGLE DEVIATIONS. 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 LEU A 5 42.54 -105.53 REMARK 500 GLU A 34 -174.94 -52.63 REMARK 500 LYS A 45 136.70 -175.61 REMARK 500 PRO A 81 -17.81 -30.67 REMARK 500 ALA A 82 136.13 165.63 REMARK 500 ASN A 83 131.39 -37.89 REMARK 500 PRO B 9 69.62 -65.43 REMARK 500 GLU B 35 145.89 -8.14 REMARK 500 VAL B 36 105.92 172.80 REMARK 500 ILE B 50 127.80 155.72 REMARK 500 CYS B 67 37.41 30.66 REMARK 500 THR B 74 128.07 -22.27 REMARK 500 PRO B 79 102.08 -53.35 REMARK 500 PRO B 81 35.61 -56.83 REMARK 500 ALA B 82 139.79 152.74 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 PRO B 81 ALA B 82 -146.76 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 TYR B 59 0.07 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 LYS B 43 -11.65 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 AB1 B 1001 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1RPI RELATED DB: PDB REMARK 900 RELATED ID: 1RQ9 RELATED DB: PDB DBREF 1RV7 A 1 99 UNP Q9QM22 Q9QM22_9HIV1 1 99 DBREF 1RV7 B 1 99 UNP Q9QM22 Q9QM22_9HIV1 1 99 SEQADV 1RV7 ASN A 25 UNP Q9QM22 ASP 25 ENGINEERED MUTATION SEQADV 1RV7 VAL A 36 UNP Q9QM22 MET 36 ENGINEERED MUTATION SEQADV 1RV7 VAL A 84 UNP Q9QM22 ILE 84 ENGINEERED MUTATION SEQADV 1RV7 ASN B 25 UNP Q9QM22 ASP 25 ENGINEERED MUTATION SEQADV 1RV7 VAL B 36 UNP Q9QM22 MET 36 ENGINEERED MUTATION SEQADV 1RV7 VAL B 84 UNP Q9QM22 ILE 84 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 LYS GLU ALA LEU LEU ASN THR SEQRES 3 A 99 GLY ALA ASP ASP THR VAL LEU GLU GLU VAL ASN LEU PRO SEQRES 4 A 99 GLY ARG TRP LYS PRO LYS LEU ILE GLY GLY ILE GLY GLY SEQRES 5 A 99 PHE VAL LYS VAL ARG GLN TYR ASP GLN VAL 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 ALA ASN VAL ILE GLY ARG ASN LEU MET THR SEQRES 8 A 99 GLN ILE 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 ILE GLY GLY GLN LEU LYS GLU ALA LEU LEU ASN THR SEQRES 3 B 99 GLY ALA ASP ASP THR VAL LEU GLU GLU VAL ASN LEU PRO SEQRES 4 B 99 GLY ARG TRP LYS PRO LYS LEU ILE GLY GLY ILE GLY GLY SEQRES 5 B 99 PHE VAL LYS VAL ARG GLN TYR ASP GLN VAL 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 ALA ASN VAL ILE GLY ARG ASN LEU MET THR SEQRES 8 B 99 GLN ILE GLY CYS THR LEU ASN PHE HET AB1 B1001 46 HETNAM AB1 N-{1-BENZYL-4-[2-(2,6-DIMETHYL-PHENOXY)-ACETYLAMINO]-3- HETNAM 2 AB1 HYDROXY-5-PHENYL-PENTYL}-3-METHYL-2-(2-OXO-TETRAHYDRO- HETNAM 3 AB1 PYRIMIDIN-1-YL)-BUTYRAMIDE HETSYN AB1 ABT-378; LOPINAVIR FORMUL 3 AB1 C37 H48 N4 O5 FORMUL 4 HOH *36(H2 O) HELIX 1 1 ARG A 87 THR A 91 1 5 HELIX 2 2 LYS B 14 GLN B 18 5 5 HELIX 3 3 GLY B 86 GLY B 94 1 9 SHEET 1 A 4 GLN A 2 THR A 4 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 4 VAL A 32 LEU A 33 0 SHEET 2 B 4 HIS A 69 VAL A 77 1 O LEU A 76 N LEU A 33 SHEET 3 B 4 PHE A 53 ILE A 66 -1 N ILE A 64 O VAL A 71 SHEET 4 B 4 LYS A 43 GLY A 48 -1 N LYS A 45 O VAL A 56 SHEET 1 C 6 VAL A 32 LEU A 33 0 SHEET 2 C 6 HIS A 69 VAL A 77 1 O LEU A 76 N LEU A 33 SHEET 3 C 6 PHE A 53 ILE A 66 -1 N ILE A 64 O VAL A 71 SHEET 4 C 6 ILE A 10 ILE A 15 -1 N LYS A 14 O GLU A 65 SHEET 5 C 6 GLN A 18 ASN A 25 -1 O GLN A 18 N ILE A 15 SHEET 6 C 6 VAL A 84 GLY A 86 1 O ILE A 85 N ASN A 25 SHEET 1 D 3 ILE B 10 ILE B 13 0 SHEET 2 D 3 LYS B 20 LEU B 24 -1 O ALA B 22 N VAL B 11 SHEET 3 D 3 VAL B 84 ILE B 85 1 O ILE B 85 N LEU B 23 SHEET 1 E 4 VAL B 32 LEU B 33 0 SHEET 2 E 4 HIS B 69 VAL B 77 1 O LEU B 76 N LEU B 33 SHEET 3 E 4 VAL B 54 ILE B 66 -1 N ARG B 57 O VAL B 77 SHEET 4 E 4 LYS B 43 ILE B 47 -1 N LYS B 45 O VAL B 56 SITE 1 AC1 12 ASN A 25 GLY A 27 GLN A 61 THR A 80 SITE 2 AC1 12 PRO A 81 ALA A 82 VAL A 84 LEU B 23 SITE 3 AC1 12 THR B 80 PRO B 81 ALA B 82 VAL B 84 CRYST1 44.975 44.975 103.676 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 0.022235 0.000000 0.000000 0.00000 SCALE2 0.000000 0.022235 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009645 0.00000