HEADER HYDROLASE 11-JAN-06 2FNT TITLE CRYSTAL STRUCTURE OF A DRUG-RESISTANT (V82A) INACTIVE (D25N) HIV-1 TITLE 2 PROTEASE COMPLEXED WITH AP2V VARIANT OF HIV-1 NC-P1 SUBSTRATE. COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: RETROPEPSIN, PR; COMPND 5 EC: 3.4.23.16; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: NC-P1 SUBSTRATE PEPTIDE; COMPND 10 CHAIN: P; COMPND 11 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HUMAN IMMUNODEFICIENCY VIRUS 1; SOURCE 3 ORGANISM_TAXID: 11676; SOURCE 4 STRAIN: HXB2; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: TAP106; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PXC35; SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES; SOURCE 12 OTHER_DETAILS: THIS SEQUENCE OCCURS NATURALLY IN DRUG-RESISTANT HIV KEYWDS STRUCTURAL INTERMEDIATE, SUBSTRATE RECOGNITION, HIV-1 PROTEASE, NC-P1 KEYWDS 2 SUBSTRATE, DRUG RESISTANCE, FLAP CONFORMATION, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR M.PRABU-JEYABALN,E.A.NALIVAIKA,C.A.SCHIFFER REVDAT 5 30-AUG-23 2FNT 1 REMARK REVDAT 4 20-OCT-21 2FNT 1 REMARK SEQADV REVDAT 3 18-OCT-17 2FNT 1 REMARK REVDAT 2 24-FEB-09 2FNT 1 VERSN REVDAT 1 05-SEP-06 2FNT 0 JRNL AUTH M.PRABU-JEYABALAN,E.A.NALIVAIKA,K.ROMANO,C.A.SCHIFFER JRNL TITL MECHANISM OF SUBSTRATE RECOGNITION BY DRUG-RESISTANT HUMAN JRNL TITL 2 IMMUNODEFICIENCY VIRUS TYPE 1 PROTEASE VARIANTS REVEALED BY JRNL TITL 3 A NOVEL STRUCTURAL INTERMEDIATE. JRNL REF J.VIROL. V. 80 3607 2006 JRNL REFN ISSN 0022-538X JRNL PMID 16537628 JRNL DOI 10.1128/JVI.80.7.3607-3616.2006 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH M.PRABU-JEYABALN,E.A.NALIVAIKA,N.M.KING,C.A.SCHIFFER REMARK 1 TITL STRUCTURAL BASIS FOR COEVOLUTION OF A HUMAN IMMUNODEFICIENCY REMARK 1 TITL 2 VIRUS TYPE 1 NUCLEOCAPSID-P1 CLEAVAGE SITE WITH A V82A REMARK 1 TITL 3 DRUG-RESISTANT MUTATION IN VIRAL PROTEASE. REMARK 1 REF J.VIROL. V. 78 12446 2004 REMARK 1 REFN ISSN 0022-538X REMARK 2 REMARK 2 RESOLUTION. 1.44 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0005 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) : 1.44 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.88 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 31723 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) : 0.188 REMARK 3 R VALUE (WORKING SET) : 0.187 REMARK 3 FREE R VALUE : 0.214 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1662 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) : 1.44 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.48 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2351 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.1820 REMARK 3 BIN FREE R VALUE SET COUNT : 124 REMARK 3 BIN FREE R VALUE : 0.2070 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1529 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 42 REMARK 3 SOLVENT ATOMS : 179 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 17.78 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.03000 REMARK 3 B22 (A**2) : -0.22000 REMARK 3 B33 (A**2) : 1.25000 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): 0.079 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.078 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.047 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.404 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.959 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.947 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1808 ; 0.007 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 1727 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2486 ; 1.320 ; 1.996 REMARK 3 BOND ANGLES OTHERS (DEGREES): 4008 ; 0.665 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 244 ; 7.200 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 62 ;36.703 ;25.161 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 292 ;13.096 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 8 ;14.237 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 288 ; 0.079 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2063 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 325 ; 0.002 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 282 ; 0.208 ; 0.300 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 1772 ; 0.194 ; 0.300 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 822 ; 0.175 ; 0.500 REMARK 3 NON-BONDED TORSION OTHERS (A): 1049 ; 0.088 ; 0.500 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 255 ; 0.264 ; 0.500 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): 30 ; 0.190 ; 0.300 REMARK 3 SYMMETRY VDW OTHERS (A): 90 ; 0.237 ; 0.300 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 42 ; 0.222 ; 0.500 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): 1494 ; 0.962 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 481 ; 0.221 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1902 ; 1.200 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 702 ; 1.886 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 584 ; 2.643 ; 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 : 1.20 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 2FNT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-JAN-06. REMARK 100 THE DEPOSITION ID IS D_1000036096. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-JUN-03 REMARK 200 TEMPERATURE (KELVIN) : 200.0 REMARK 200 PH : 6.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 5.0.2 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 : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : R-AXIS REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 33155 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.440 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 (%) : 100.0 REMARK 200 DATA REDUNDANCY : 9.000 REMARK 200 R MERGE (I) : 0.04700 REMARK 200 R SYM (I) : 0.04700 REMARK 200 FOR THE DATA SET : 10.4000 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: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 1T3R REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.11 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.99 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 126MM SODIUM PHOSPHATE PH 6.2; 63MM REMARK 280 SODIUM CITRATE; AMMONIUM SULPHATE, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 298K 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 25.52800 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 30.73750 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 28.81150 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 30.73750 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 25.52800 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 28.81150 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 6350 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9520 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -60.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, P 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 LYS P 9 REMARK 465 ILE P 10 REMARK 465 ASN P 11 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 GLU A 21 CG CD OE1 OE2 REMARK 470 ASN A 37 CG OD1 ND2 REMARK 470 LYS A 70 CG CD CE NZ REMARK 470 LYS B 41 CG CD CE NZ REMARK 470 LYS B 43 CG CD CE NZ REMARK 470 LYS B 45 CG CD CE NZ REMARK 470 GLU B 65 CG CD OE1 OE2 REMARK 470 LYS B 70 CG CD CE NZ REMARK 470 ARG P 2 CG CD NE CZ NH1 NH2 REMARK 470 GLN P 3 CG CD OE1 NE2 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 LYS A 41 CD CE NZ REMARK 480 LYS A 43 CE NZ REMARK 480 LYS A 55 CD CE NZ REMARK 480 LYS B 7 CE NZ REMARK 480 LYS B 55 CE NZ 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 LYS A 55 CG LYS A 55 CD -0.437 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 LYS A 55 CB - CG - CD ANGL. DEV. = 19.7 DEGREES REMARK 500 PRO B 39 C - N - CA ANGL. DEV. = 11.6 DEGREES REMARK 500 PRO B 39 C - N - CA ANGL. DEV. = 10.3 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 GLU A 35 80.25 41.68 REMARK 500 MET A 36 -50.34 -121.07 REMARK 500 ASN A 37 109.77 47.86 REMARK 500 PRO B 39 125.85 -36.80 REMARK 500 PRO B 39 -116.97 -38.59 REMARK 500 ASN P 5 38.71 -90.89 REMARK 500 PHE P 6 157.17 -46.94 REMARK 500 LEU P 7 116.56 -170.27 REMARK 500 REMARK 500 REMARK: NULL REMARK 615 REMARK 615 ZERO OCCUPANCY ATOM REMARK 615 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 615 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 615 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 615 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 615 M RES C SSEQI REMARK 615 HOH B 589 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 B 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 B 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 505 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 506 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 507 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 B 508 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT B 509 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 510 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1TSQ RELATED DB: PDB REMARK 900 FLAPS CLOSED CONFORMATION OF THE DRUG-RESISTANT (V82A)/INACTIVE REMARK 900 (D25N) HIV-1 PROTEASE COMPLEXED WITH AP2V VARIANT OF NC-P1 REMARK 900 SUBSTRATE. REMARK 900 RELATED ID: 2FNS RELATED DB: PDB DBREF 2FNT A 1 99 UNP O38716 O38716_9HIV1 1 99 DBREF 2FNT B 1 99 UNP O38716 O38716_9HIV1 1 99 DBREF 2FNT P 2 11 PDB 2FNT 2FNT 2 11 SEQADV 2FNT LYS A 7 UNP O38716 GLN 7 ENGINEERED MUTATION SEQADV 2FNT ASN A 25 UNP O38716 ASP 25 ENGINEERED MUTATION SEQADV 2FNT VAL A 64 UNP O38716 ILE 64 ENGINEERED MUTATION SEQADV 2FNT ALA A 82 UNP O38716 VAL 82 ENGINEERED MUTATION SEQADV 2FNT LYS B 7 UNP O38716 GLN 7 ENGINEERED MUTATION SEQADV 2FNT ASN B 25 UNP O38716 ASP 25 ENGINEERED MUTATION SEQADV 2FNT VAL B 64 UNP O38716 ILE 64 ENGINEERED MUTATION SEQADV 2FNT ALA B 82 UNP O38716 VAL 82 ENGINEERED MUTATION SEQRES 1 A 99 PRO GLN ILE THR LEU TRP LYS ARG PRO LEU VAL THR ILE SEQRES 2 A 99 ARG 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 MET ASN LEU PRO SEQRES 4 A 99 GLY LYS 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 PRO VAL 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 ALA ASN ILE ILE GLY ARG ASN LEU LEU THR SEQRES 8 A 99 GLN ILE GLY CYS 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 ARG 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 MET ASN LEU PRO SEQRES 4 B 99 GLY LYS 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 PRO VAL 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 ALA ASN ILE ILE GLY ARG ASN LEU LEU THR SEQRES 8 B 99 GLN ILE GLY CYS THR LEU ASN PHE SEQRES 1 P 10 ARG GLN VAL ASN PHE LEU GLY LYS ILE ASN HET ACT A 504 8 HET PO4 A 505 5 HET PO4 A 506 5 HET PO4 A 507 5 HET ACT A 510 4 HET PO4 B 501 5 HET PO4 B 502 5 HET PO4 B 508 5 HET ACT B 509 8 HETNAM ACT ACETATE ION HETNAM PO4 PHOSPHATE ION FORMUL 4 ACT 3(C2 H3 O2 1-) FORMUL 5 PO4 6(O4 P 3-) FORMUL 13 HOH *179(H2 O) HELIX 1 1 GLY A 86 THR A 91 1 6 HELIX 2 2 GLY B 86 THR B 91 1 6 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 THR A 96 O ASN B 98 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 VAL A 77 -1 O GLY A 73 N ILE A 62 SHEET 4 B 8 VAL A 32 LEU A 33 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 LEU A 10 ILE 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 ARG 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 ILE B 54 N ILE B 47 SHEET 3 C 8 HIS B 69 VAL B 77 -1 O HIS B 69 N ILE B 66 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 LEU B 10 ILE 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 ARG B 14 SITE 1 AC1 7 PRO A 1 GLY B 68 HIS B 69 LYS B 70 SITE 2 AC1 7 HOH B 519 HOH B 537 HOH B 572 SITE 1 AC2 4 LYS B 20 GLU B 21 ASN B 83 HOH B 554 SITE 1 AC3 3 LYS A 7 ARG A 8 ARG B 87 SITE 1 AC4 4 LYS A 20 GLU A 21 ASN A 83 HOH A 539 SITE 1 AC5 7 TRP A 6 GLY A 51 HOH A 571 THR B 91 SITE 2 AC5 7 GLY B 94 HOH B 512 HOH B 521 SITE 1 AC6 8 GLY A 16 PRO A 63 HOH A 546 GLY B 16 SITE 2 AC6 8 GLY B 17 HOH B 520 HOH B 530 HOH B 585 SITE 1 AC7 5 LEU B 19 PRO B 44 LYS B 45 MET B 46 SITE 2 AC7 5 HOH B 586 SITE 1 AC8 2 LYS B 7 ARG B 8 SITE 1 AC9 3 GLN A 58 HOH A 563 GLN B 61 CRYST1 51.056 57.623 61.475 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 0.019586 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017354 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016267 0.00000