HEADER HYDROLASE 27-OCT-06 2NPH TITLE CRYSTAL STRUCTURE OF HIV1 PROTEASE IN SITU PRODUCT COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEASE RETROPEPSIN; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: HIV-1 PROTEASE; COMPND 5 EC: 3.4.23.16; COMPND 6 ENGINEERED: YES; COMPND 7 OTHER_DETAILS: OBSERVATION OF A LOW BARRIER HYDROGEN BOND BETWEEN COMPND 8 CATALYTIC ASPARTATES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: TETRAPEPTIDE FRAGMENT; COMPND 11 CHAIN: S; COMPND 12 ENGINEERED: YES; COMPND 13 MOL_ID: 3; COMPND 14 MOLECULE: PENTAPEPTIDE FRAGMENT; COMPND 15 CHAIN: T; COMPND 16 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 BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21DE3; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET11A; SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES; SOURCE 12 MOL_ID: 3; SOURCE 13 SYNTHETIC: YES KEYWDS ANTI-PARALLEL BETA SHEET, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR M.V.HOSUR,A.DAS,V.PRASHAR REVDAT 6 27-DEC-23 2NPH 1 REMARK REVDAT 5 20-OCT-21 2NPH 1 SEQADV REVDAT 4 31-JAN-18 2NPH 1 JRNL REVDAT 3 18-OCT-17 2NPH 1 REMARK REVDAT 2 24-FEB-09 2NPH 1 VERSN REVDAT 1 19-DEC-06 2NPH 0 JRNL AUTH A.DAS,V.PRASHAR,S.MAHALE,L.SERRE,J.-L.FERRER,M.V.HOSUR JRNL TITL CRYSTAL STRUCTURE OF HIV-1 PROTEASE IN SITU PRODUCT COMPLEX JRNL TITL 2 AND OBSERVATION OF A LOW-BARRIER HYDROGEN BOND BETWEEN JRNL TITL 3 CATALYTIC ASPARTATES JRNL REF PROC.NATL.ACAD.SCI.USA V. 103 18464 2006 JRNL REFN ISSN 0027-8424 JRNL PMID 17116869 JRNL DOI 10.1073/PNAS.0605809103 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH M.KUMAR,V.PRASHAR,S.MAHALE,M.V.HOSUR REMARK 1 TITL OBSERVATION OF A TETRAHEDRAL REACTION INTERMEDIATE IN HIV-1 REMARK 1 TITL 2 PROTEASE SUBSTRATE COMPLEX REMARK 1 REF BIOCHEM.J. V. 389 365 2005 REMARK 1 REFN ISSN 0264-6021 REMARK 1 REFERENCE 2 REMARK 1 AUTH B.PILLAI,S.V.BHAT,K.K.KANNAN,M.V.HOSUR REMARK 1 TITL RAPID SCREENING FOR HIV-1 PROTEASE INHIBITOR LEADS THROUGH REMARK 1 TITL 2 X-RAY DIFFRACTION REMARK 1 REF ACTA CRYSTALLOGR.,SECT.D V. 60 594 2004 REMARK 1 REFN ISSN 0907-4449 REMARK 1 REFERENCE 3 REMARK 1 AUTH B.PILLAI,K.K.KANNAN,M.V.HOSUR REMARK 1 TITL 1.9A X-RAY STUDY SHOWS CLOSED FLAP CONFORMATION IN CRYSTALS REMARK 1 TITL 2 OF TETHERED HIV-1 PR REMARK 1 REF PROTEINS V. 43 57 2001 REMARK 1 REFN ISSN 0887-3585 REMARK 1 REFERENCE 4 REMARK 1 AUTH M.KUMAR,K.K.KANNAN,M.V.HOSUR,N.S.BHAVESH,A.CHATTERJEE, REMARK 1 AUTH 2 R.MITTAL,R.V.HOSUR REMARK 1 TITL EFFECTS OF REMOTE MUTATION ON THE AUTOLYSIS OF HIV-1 PR: REMARK 1 TITL 2 X-RAY AND NMR INVESTIGATIONS REMARK 1 REF BIOCHEM.BIOPHYS.RES.COMMUN. V. 294 395 2002 REMARK 1 REFN ISSN 0006-291X REMARK 2 REMARK 2 RESOLUTION. 1.65 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) : 1.65 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.53 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 20326 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) : 0.216 REMARK 3 R VALUE (WORKING SET) : 0.214 REMARK 3 FREE R VALUE : 0.259 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1069 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) : 1.65 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.69 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1501 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.3020 REMARK 3 BIN FREE R VALUE SET COUNT : 79 REMARK 3 BIN FREE R VALUE : 0.3150 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1585 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 156 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 39.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 33.43 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.36000 REMARK 3 B22 (A**2) : 0.36000 REMARK 3 B33 (A**2) : -0.54000 REMARK 3 B12 (A**2) : 0.18000 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): 0.130 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.127 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.097 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.895 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.957 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.935 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1611 ; 0.015 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2183 ; 1.546 ; 1.989 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 203 ; 5.207 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 58 ;40.938 ;24.828 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 290 ;12.526 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 8 ;14.582 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 260 ; 0.104 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1163 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 823 ; 0.253 ; 0.300 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1113 ; 0.331 ; 0.500 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 190 ; 0.283 ; 0.700 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): 82 ; 0.288 ; 0.300 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 38 ; 0.760 ; 0.700 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): 1041 ; 1.160 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1652 ; 1.945 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 634 ; 2.941 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 531 ; 4.892 ; 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 : 4 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 1 A 99 REMARK 3 RESIDUE RANGE : B 1001 B 1099 REMARK 3 ORIGIN FOR THE GROUP (A): -11.3595 19.7577 27.6314 REMARK 3 T TENSOR REMARK 3 T11: -0.0561 T22: -0.0027 REMARK 3 T33: -0.0374 T12: -0.0396 REMARK 3 T13: -0.0121 T23: -0.0068 REMARK 3 L TENSOR REMARK 3 L11: 2.8083 L22: 1.1209 REMARK 3 L33: 1.8569 L12: 1.5143 REMARK 3 L13: 2.2714 L23: 1.3023 REMARK 3 S TENSOR REMARK 3 S11: 0.0014 S12: -0.0063 S13: -0.0667 REMARK 3 S21: -0.0113 S22: 0.0283 S23: -0.0373 REMARK 3 S31: 0.0012 S32: 0.0131 S33: -0.0297 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 0 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 ORIGIN FOR THE GROUP (A): 0.0000 0.0000 0.0000 REMARK 3 T TENSOR REMARK 3 T11: 0.0000 T22: 0.0000 REMARK 3 T33: 0.0000 T12: 0.0000 REMARK 3 T13: 0.0000 T23: 0.0000 REMARK 3 L TENSOR REMARK 3 L11: 0.0000 L22: 0.0000 REMARK 3 L33: 0.0000 L12: 0.0000 REMARK 3 L13: 0.0000 L23: 0.0000 REMARK 3 S TENSOR REMARK 3 S11: 0.0000 S12: 0.0000 S13: 0.0000 REMARK 3 S21: 0.0000 S22: 0.0000 S23: 0.0000 REMARK 3 S31: 0.0000 S32: 0.0000 S33: 0.0000 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : S 1 S 4 REMARK 3 RESIDUE RANGE : T 5 T 9 REMARK 3 ORIGIN FOR THE GROUP (A): -8.1150 14.9498 26.8550 REMARK 3 T TENSOR REMARK 3 T11: -0.0009 T22: 0.0004 REMARK 3 T33: -0.0018 T12: -0.0007 REMARK 3 T13: -0.0007 T23: -0.0019 REMARK 3 L TENSOR REMARK 3 L11: 10.5838 L22: 12.4109 REMARK 3 L33: 23.3387 L12: 11.4536 REMARK 3 L13: -14.3140 L23: -15.7430 REMARK 3 S TENSOR REMARK 3 S11: -0.2695 S12: 0.0426 S13: -1.3048 REMARK 3 S21: -0.2896 S22: 0.2070 S23: -1.1424 REMARK 3 S31: 0.1841 S32: 0.4474 S33: 0.0625 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 0 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 ORIGIN FOR THE GROUP (A): 0.0000 0.0000 0.0000 REMARK 3 T TENSOR REMARK 3 T11: 0.0000 T22: 0.0000 REMARK 3 T33: 0.0000 T12: 0.0000 REMARK 3 T13: 0.0000 T23: 0.0000 REMARK 3 L TENSOR REMARK 3 L11: 0.0000 L22: 0.0000 REMARK 3 L33: 0.0000 L12: 0.0000 REMARK 3 L13: 0.0000 L23: 0.0000 REMARK 3 S TENSOR REMARK 3 S11: 0.0000 S12: 0.0000 S13: 0.0000 REMARK 3 S21: 0.0000 S22: 0.0000 S23: 0.0000 REMARK 3 S31: 0.0000 S32: 0.0000 S33: 0.0000 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : 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 2NPH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-NOV-06. REMARK 100 THE DEPOSITION ID IS D_1000040143. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : BM30A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97945 REMARK 200 MONOCHROMATOR : SI 111 REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20326 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.650 REMARK 200 RESOLUTION RANGE LOW (A) : 32.530 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.0 REMARK 200 DATA REDUNDANCY : 5.530 REMARK 200 R MERGE (I) : 0.08100 REMARK 200 R SYM (I) : 0.08100 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 10.1600 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 <I/SIGMA(I)> 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: CNS REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.69 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.01 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: AMMONIUM SULFATE PRECIPITANT, PH 6.2, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 27.26000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 54.52000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 40.89000 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 68.15000 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 13.63000 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 300 REMARK: THE FUNCTIONAL DIMER IS IN THE ASYMMETRIC UNIT. 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5480 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9140 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -26.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, S, T 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 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 MET B1095 CG SD CE 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 B 319 O HOH B 373 1.21 REMARK 500 O HOH B 330 O HOH B 381 1.30 REMARK 500 O HOH A 468 O HOH A 469 1.37 REMARK 500 NZ LYS A 20 O HOH A 399 1.56 REMARK 500 O HOH A 409 O HOH A 424 1.58 REMARK 500 O HOH B 391 O HOH B 463 1.72 REMARK 500 O HOH A 310 O HOH A 370 1.87 REMARK 500 O GLU A 35 O HOH A 406 1.96 REMARK 500 SG CYS B 1067 O HOH B 488 1.98 REMARK 500 O MET B 1095 O HOH B 395 2.11 REMARK 500 O HOH A 455 O HOH B 458 2.11 REMARK 500 O TRP A 42 O HOH A 421 2.11 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 HOH A 316 O HOH B 475 6665 1.16 REMARK 500 O HOH A 345 O HOH B 395 2665 1.34 REMARK 500 O HOH A 447 O HOH B 494 2565 1.44 REMARK 500 O HOH A 344 O HOH B 393 2665 1.52 REMARK 500 O HOH A 398 O HOH A 500 2665 1.69 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 48.73 -71.48 REMARK 500 PRO B1044 155.62 -48.15 REMARK 500 PRO B1079 42.32 -75.07 REMARK 500 THR S 3 72.04 -100.00 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1G6L RELATED DB: PDB REMARK 900 UNLIGANDED CLOSED-FLAP STRUCTURE OF TETHERED HIV-1 PR REMARK 900 RELATED ID: 1LV1 RELATED DB: PDB REMARK 900 UNLIGANDED CLOSED-FLAP STRUCTURE OF C1095A MUTANT OF TETHERED HIV-1 REMARK 900 PR DBREF 2NPH A 1 99 UNP Q72874 Q72874_9HIV1 1 99 DBREF 2NPH B 1001 1099 UNP Q72874 Q72874_9HIV1 1 99 DBREF 2NPH S 1 4 PDB 2NPH 2NPH 1 4 DBREF 2NPH T 5 9 PDB 2NPH 2NPH 5 9 SEQADV 2NPH MET A 95 UNP Q72874 CYS 95 ENGINEERED MUTATION SEQADV 2NPH MET B 1095 UNP Q72874 CYS 95 ENGINEERED MUTATION SEQRES 1 A 99 PRO GLN VAL THR LEU TRP GLN ARG PRO LEU VAL THR ILE SEQRES 2 A 99 LYS ILE GLY GLY GLN LEU LYS GLU ALA LEU LEU ASP THR SEQRES 3 A 99 GLY ALA ASP ASP THR VAL LEU GLU GLU MET SER LEU PRO SEQRES 4 A 99 GLY ARG 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 LEU ILE 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 VAL ASN ILE ILE GLY ARG ASN LEU LEU THR SEQRES 8 A 99 GLN ILE GLY MET THR LEU ASN PHE SEQRES 1 B 99 PRO GLN VAL THR LEU TRP GLN ARG PRO LEU VAL THR ILE SEQRES 2 B 99 LYS ILE GLY GLY GLN LEU LYS GLU ALA LEU LEU ASP THR SEQRES 3 B 99 GLY ALA ASP ASP THR VAL LEU GLU GLU MET SER LEU PRO SEQRES 4 B 99 GLY ARG 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 LEU ILE 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 VAL ASN ILE ILE GLY ARG ASN LEU LEU THR SEQRES 8 B 99 GLN ILE GLY MET THR LEU ASN PHE SEQRES 1 S 4 ALA GLU THR PHE SEQRES 1 T 5 TYR VAL ASP GLY ALA FORMUL 5 HOH *156(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 1086 THR B 1091 1 6 HELIX 4 4 GLN B 1092 GLY B 1094 5 3 SHEET 1 A 4 VAL A 3 THR A 4 0 SHEET 2 A 4 THR B1096 ASN B1098 -1 O LEU B1097 N VAL A 3 SHEET 3 A 4 THR A 96 ASN A 98 -1 N ASN A 98 O THR B1096 SHEET 4 A 4 GLN B1002 THR B1004 -1 O VAL B1003 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 VAL A 56 N LYS A 45 SHEET 3 B 8 HIS A 69 VAL A 77 -1 O HIS A 69 N ILE A 66 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 VAL A 11 O ALA A 22 SHEET 8 B 8 GLY A 52 ILE A 66 -1 O GLU A 65 N LYS A 14 SHEET 1 C 8 LYS B1043 GLY B1049 0 SHEET 2 C 8 GLY B1052 ILE B1066 -1 O GLY B1052 N GLY B1049 SHEET 3 C 8 HIS B1069 VAL B1077 -1 O VAL B1077 N ARG B1057 SHEET 4 C 8 VAL B1032 LEU B1033 1 N LEU B1033 O LEU B1076 SHEET 5 C 8 ILE B1084 ILE B1085 -1 O ILE B1084 N VAL B1032 SHEET 6 C 8 GLN B1018 LEU B1024 1 N LEU B1023 O ILE B1085 SHEET 7 C 8 LEU B1010 ILE B1015 -1 N ILE B1013 O LYS B1020 SHEET 8 C 8 GLY B1052 ILE B1066 -1 O GLU B1065 N LYS B1014 CRYST1 62.030 62.030 81.780 90.00 90.00 120.00 P 61 12 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 0.016121 0.009308 0.000000 0.00000 SCALE2 0.000000 0.018615 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012228 0.00000