10 20 30 40 50 60 70 80 2NPH - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER 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 COMPND 8 BETWEEN 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 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, JRNL AUTH 2 M.V.HOSUR JRNL TITL CRYSTAL STRUCTURE OF HIV-1 PROTEASE IN SITU JRNL TITL 2 PRODUCT COMPLEX AND OBSERVATION OF A LOW-BARRIER JRNL TITL 3 HYDROGEN BOND BETWEEN 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,HOSUR M.V. REMARK 1 TITL OBSERVATION OF A TETRAHEDRAL REACTION INTERMEDIATE REMARK 1 TITL 2 IN HIV-1 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 REMARK 1 TITL 2 THROUGH 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 REMARK 1 TITL 2 CRYSTALS 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, REMARK 1 AUTH 2 A.CHATTERJEE,R.MITTAL,R.V.HOSUR REMARK 1 TITL EFFECTS OF REMOTE MUTATION ON THE AUTOLYSIS OF REMARK 1 TITL 2 HIV-1 PR: 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 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON 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) (%) : 100.00 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 SIDE-CHAIN BOND REFINED ATOMS (A**2): 634 ; 2.941 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 531 ; 4.892 ; 4.500 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 REMARK 3 RIDING POSITIONS
REMARK 4 REMARK 4 2NPH COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-NOV-06. REMARK 100 THE RCSB ID CODE IS RCSB040143.
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 REMARK 280 6.2, 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 B 395 O HOH A 345 3564 1.34 REMARK 500 O HOH B 494 O HOH A 447 3454 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 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 341 DISTANCE = 10.35 ANGSTROMS REMARK 525 HOH A 350 DISTANCE = 8.43 ANGSTROMS REMARK 525 HOH A 351 DISTANCE = 11.77 ANGSTROMS REMARK 525 HOH A 423 DISTANCE = 8.33 ANGSTROMS REMARK 525 HOH A 425 DISTANCE = 9.19 ANGSTROMS REMARK 525 HOH B 492 DISTANCE = 8.47 ANGSTROMS REMARK 525 HOH B 493 DISTANCE = 5.77 ANGSTROMS REMARK 525 HOH A 496 DISTANCE = 8.68 ANGSTROMS REMARK 525 HOH A 497 DISTANCE = 8.87 ANGSTROMS REMARK 525 HOH A 498 DISTANCE = 7.96 ANGSTROMS
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 REMARK 900 TETHERED HIV-1 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 SEQADV 2NPH MET B 1095 UNP Q72874 CYS 95 ENGINEERED
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