HEADER HYDROLASE/HYDROLASE INHIBITOR 27-JAN-98 1A30
TITLE HIV-1 PROTEASE COMPLEXED WITH A TRIPEPTIDE INHIBITOR
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: HIV-1 PROTEASE;
COMPND 3 CHAIN: A, B;
COMPND 4 EC: 3.4.23.16;
COMPND 5 ENGINEERED: YES;
COMPND 6 MUTATION: YES;
COMPND 7 MOL_ID: 2;
COMPND 8 MOLECULE: TRIPEPTIDE GLU-ASP-LEU;
COMPND 9 CHAIN: C;
COMPND 10 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: HUMAN IMMUNODEFICIENCY VIRUS 1;
SOURCE 3 ORGANISM_TAXID: 11676;
SOURCE 4 STRAIN: ISOLATE HXB2;
SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21;
SOURCE 6 EXPRESSION_SYSTEM_TAXID: 511693;
SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21;
SOURCE 8 EXPRESSION_SYSTEM_VECTOR: PET-11 A;
SOURCE 9 MOL_ID: 2
KEYWDS ASPARTIC PROTEASE, HIV PROTEASE, HYDROLASE-HYDROLASE INHIBITOR
KEYWDS 2 COMPLEX
EXPDTA X-RAY DIFFRACTION
AUTHOR J.M.LOUIS,F.DYDA,N.T.NASHED,A.R.KIMMEL,D.R.DAVIES
REVDAT 5 07-FEB-24 1A30 1 REMARK
REVDAT 4 03-NOV-21 1A30 1 SEQADV
REVDAT 3 13-JUL-11 1A30 1 VERSN
REVDAT 2 24-FEB-09 1A30 1 VERSN
REVDAT 1 29-APR-98 1A30 0
JRNL AUTH J.M.LOUIS,F.DYDA,N.T.NASHED,A.R.KIMMEL,D.R.DAVIES
JRNL TITL HYDROPHILIC PEPTIDES DERIVED FROM THE TRANSFRAME REGION OF
JRNL TITL 2 GAG-POL INHIBIT THE HIV-1 PROTEASE.
JRNL REF BIOCHEMISTRY V. 37 2105 1998
JRNL REFN ISSN 0006-2960
JRNL PMID 9485357
JRNL DOI 10.1021/BI972059X
REMARK 2
REMARK 2 RESOLUTION. 2.00 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : X-PLOR 3.1
REMARK 3 AUTHORS : BRUNGER
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 15.00
REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000
REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 100000.000
REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.1000
REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 97.3
REMARK 3 NUMBER OF REFLECTIONS : 13987
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 SET) : 0.189
REMARK 3 FREE R VALUE : 0.227
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000
REMARK 3 FREE R VALUE TEST SET COUNT : 724
REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.008
REMARK 3
REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN.
REMARK 3 TOTAL NUMBER OF BINS USED : 8
REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.00
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.09
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 64.97
REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1238
REMARK 3 BIN R VALUE (WORKING SET) : 0.2700
REMARK 3 BIN FREE R VALUE : 0.2998
REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.31
REMARK 3 BIN FREE R VALUE TEST SET COUNT : 59
REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.003
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 1536
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 0
REMARK 3 SOLVENT ATOMS : 216
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 21.71
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.12
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : 1.00000
REMARK 3 B22 (A**2) : 1.00000
REMARK 3 B33 (A**2) : 1.00000
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 COORDINATE ERROR.
REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL
REMARK 3 ESD FROM SIGMAA (A) : NULL
REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL
REMARK 3
REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR.
REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL
REMARK 3 ESD FROM C-V SIGMAA (A) : NULL
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES.
REMARK 3 BOND LENGTHS (A) : 0.007
REMARK 3 BOND ANGLES (DEGREES) : 1.381
REMARK 3 DIHEDRAL ANGLES (DEGREES) : 26.39
REMARK 3 IMPROPER ANGLES (DEGREES) : 1.230
REMARK 3
REMARK 3 ISOTROPIC THERMAL MODEL : NULL
REMARK 3
REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA
REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL
REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL
REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL
REMARK 3
REMARK 3 NCS MODEL : NULL
REMARK 3
REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT
REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL
REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL
REMARK 3
REMARK 3 PARAMETER FILE 1 : PARHCSDX.PRO
REMARK 3 PARAMETER FILE 2 : PARAM19.SOL
REMARK 3 PARAMETER FILE 3 : NULL
REMARK 3 TOPOLOGY FILE 1 : TOPHCSDX.PRO
REMARK 3 TOPOLOGY FILE 2 : NULL
REMARK 3 TOPOLOGY FILE 3 : NULL
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 1A30 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL.
REMARK 100 THE DEPOSITION ID IS D_1000170328.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : MAY-96
REMARK 200 TEMPERATURE (KELVIN) : 95
REMARK 200 PH : 4.2
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 RUH2R
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418
REMARK 200 MONOCHROMATOR : NI FILTER
REMARK 200 OPTICS : YALE MIRRORS
REMARK 200
REMARK 200 DETECTOR TYPE : IMAGE PLATE
REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IIC
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO
REMARK 200 DATA SCALING SOFTWARE : SCALEPACK
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14128
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000
REMARK 200 RESOLUTION RANGE LOW (A) : 15.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 86.7
REMARK 200 DATA REDUNDANCY : 4.630
REMARK 200 R MERGE (I) : 0.04800
REMARK 200 R SYM (I) : 0.04800
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 14.6000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.06
REMARK 200 COMPLETENESS FOR SHELL (%) : 71.3
REMARK 200 DATA REDUNDANCY IN SHELL : 2.20
REMARK 200 R MERGE FOR SHELL (I) : 0.12100
REMARK 200 R SYM FOR SHELL (I) : 0.12100
REMARK 200 <I/SIGMA(I)> FOR SHELL : 5.600
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: NULL
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: USING ISOMORPHOUS TO
REMARK 200 PREVIOUS STRUCTURE
REMARK 200 SOFTWARE USED: X-PLOR 3.1
REMARK 200 STARTING MODEL: NULL
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 42.50
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.65
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: PH 4.2
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -X,-Y,Z
REMARK 290 3555 -X+1/2,Y+1/2,-Z
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 0.00000
REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 29.23500
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 43.22000
REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000
REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 29.23500
REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 43.22000
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: 4530 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 9280 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -26.0 KCAL/MOL
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C
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 ARG A 41 CG CD NE CZ NH1 NH2
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 35 116.96 -34.48
REMARK 500 PRO A 79 50.80 -69.53
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 CHAIN C OF TRIPEPTIDE GLU-ASP
REMARK 800 -LEU
DBREF 1A30 A 1 99 UNP P04585 POL_HV1H2 69 167
DBREF 1A30 B 1 99 UNP P04585 POL_HV1H2 69 167
DBREF 1A30 C 506 508 PDB 1A30 1A30 506 508
SEQADV 1A30 LYS A 7 UNP P04585 GLN 75 ENGINEERED MUTATION
SEQADV 1A30 ILE A 33 UNP P04585 LEU 101 ENGINEERED MUTATION
SEQADV 1A30 ILE A 63 UNP P04585 LEU 131 ENGINEERED MUTATION
SEQADV 1A30 LYS B 7 UNP P04585 GLN 75 ENGINEERED MUTATION
SEQADV 1A30 ILE B 33 UNP P04585 LEU 101 ENGINEERED MUTATION
SEQADV 1A30 ILE B 63 UNP P04585 LEU 131 ENGINEERED MUTATION
SEQRES 1 A 99 PRO GLN ILE THR LEU TRP LYS 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 ILE 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 ILE 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 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 LYS ILE GLY GLY GLN LEU LYS GLU ALA LEU LEU ASP THR
SEQRES 3 B 99 GLY ALA ASP ASP THR VAL ILE 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 ILE 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 CYS THR LEU ASN PHE
SEQRES 1 C 3 GLU ASP LEU
FORMUL 4 HOH *216(H2 O)
HELIX 1 1 ARG A 87 LEU A 90 1 4
HELIX 2 2 ARG B 87 LEU B 90 1 4
SHEET 1 A 4 GLN A 18 LEU A 23 0
SHEET 2 A 4 LEU A 10 ILE A 15 -1 N ILE A 15 O GLN A 18
SHEET 3 A 4 ILE A 62 ILE A 66 -1 N GLU A 65 O LYS A 14
SHEET 4 A 4 HIS A 69 GLY A 73 -1 N GLY A 73 O ILE A 62
SHEET 1 B 4 VAL A 32 GLU A 34 0
SHEET 2 B 4 VAL A 75 GLY A 78 1 N LEU A 76 O ILE A 33
SHEET 3 B 4 GLY A 52 TYR A 59 -1 N TYR A 59 O VAL A 75
SHEET 4 B 4 TRP A 42 GLY A 49 -1 N GLY A 49 O GLY A 52
SHEET 1 C 2 LEU B 10 ILE B 15 0
SHEET 2 C 2 GLN B 18 LEU B 23 -1 N ALA B 22 O VAL B 11
SHEET 1 D 3 LYS B 43 GLY B 48 0
SHEET 2 D 3 PHE B 53 TYR B 59 -1 N GLN B 58 O LYS B 43
SHEET 3 D 3 VAL B 75 GLY B 78 -1 N VAL B 77 O ARG B 57
SHEET 1 E 2 ILE B 62 ILE B 66 0
SHEET 2 E 2 HIS B 69 GLY B 73 -1 N GLY B 73 O ILE B 62
SITE 1 AC1 15 ASP A 25 GLY A 27 ALA A 28 ASP A 29
SITE 2 AC1 15 ASP A 30 ILE A 47 GLY A 48 ILE A 50
SITE 3 AC1 15 HOH A1076 ARG B 8 ASP B 25 VAL B 82
SITE 4 AC1 15 HOH C1075 HOH C1092 HOH C1097
CRYST1 58.470 86.440 45.810 90.00 90.00 90.00 P 21 21 2 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 0.017103 0.000000 0.000000 0.00000
SCALE2 0.000000 0.011569 0.000000 0.00000
SCALE3 0.000000 0.000000 0.021829 0.00000
MTRIX1 1 -0.341600 0.828700 -0.443400 0.45720 1
MTRIX2 1 0.828700 0.043000 -0.558100 14.52920 1
MTRIX3 1 -0.443400 -0.558100 -0.701400 27.83140 1
(ATOM LINES ARE NOT SHOWN.)
END