HEADER HYDROLASE/HYDROLASE INHIBITOR 18-MAY-95 1HPX
TITLE HIV-1 PROTEASE COMPLEXED WITH THE INHIBITOR KNI-272
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: HIV-1 PROTEASE;
COMPND 3 CHAIN: A, B;
COMPND 4 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: HUMAN IMMUNODEFICIENCY VIRUS 1;
SOURCE 3 ORGANISM_TAXID: 11676;
SOURCE 4 STRAIN: HIVLAI;
SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562
KEYWDS ACID PROTEASE, HYDROLASE, HYDROLASE-HYDROLASE INHIBITOR COMPLEX
EXPDTA X-RAY DIFFRACTION
AUTHOR T.N.BHAT,J.W.ERICKSON
REVDAT 5 07-FEB-24 1HPX 1 REMARK HETSYN
REVDAT 4 13-JUL-11 1HPX 1 VERSN
REVDAT 3 24-FEB-09 1HPX 1 VERSN
REVDAT 2 01-APR-03 1HPX 1 JRNL
REVDAT 1 08-MAR-96 1HPX 0
JRNL AUTH E.T.BALDWIN,T.N.BHAT,S.GULNIK,B.LIU,I.A.TOPOL,Y.KISO,
JRNL AUTH 2 T.MIMOTO,H.MITSUYA,J.W.ERICKSON
JRNL TITL STRUCTURE OF HIV-1 PROTEASE WITH KNI-272, A TIGHT-BINDING
JRNL TITL 2 TRANSITION-STATE ANALOG CONTAINING ALLOPHENYLNORSTATINE.
JRNL REF STRUCTURE V. 3 581 1995
JRNL REFN ISSN 0969-2126
JRNL PMID 8590019
JRNL DOI 10.1016/S0969-2126(01)00192-7
REMARK 1
REMARK 1 REFERENCE 1
REMARK 1 AUTH T.N.BHAT,E.T.BALDWIN,B.LIU,Y.-S.E.CHENG,J.W.ERICKSON
REMARK 1 TITL CRYSTAL STRUCTURE OF A TETHERED DIMER OF HIV-1 PROTEINASE
REMARK 1 TITL 2 COMPLEXED WITH AN INHIBITOR
REMARK 1 REF NAT.STRUCT.BIOL. V. 1 552 1994
REMARK 1 REFN ISSN 1072-8368
REMARK 1 REFERENCE 2
REMARK 1 AUTH A.WLODAWER,J.W.ERICKSON
REMARK 1 TITL STRUCTURE-BASED INHIBITORS OF HIV-1 PROTEASE
REMARK 1 REF ANNU.REV.BIOCHEM. V. 62 543 1993
REMARK 1 REFN ISSN 0066-4154
REMARK 2
REMARK 2 RESOLUTION. 2.00 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : X-PLOR
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) : 7.00
REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000
REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL
REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL
REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 86.0
REMARK 3 NUMBER OF REFLECTIONS : 9665
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 CROSS-VALIDATION METHOD : NULL
REMARK 3 FREE R VALUE TEST SET SELECTION : NULL
REMARK 3 R VALUE (WORKING SET) : 0.170
REMARK 3 FREE R VALUE : NULL
REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL
REMARK 3 FREE R VALUE TEST SET COUNT : NULL
REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL
REMARK 3
REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN.
REMARK 3 TOTAL NUMBER OF BINS USED : NULL
REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL
REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL
REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL
REMARK 3 BIN R VALUE (WORKING SET) : NULL
REMARK 3 BIN FREE R VALUE : NULL
REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL
REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL
REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 1516
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 46
REMARK 3 SOLVENT ATOMS : 6
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : NULL
REMARK 3 B22 (A**2) : NULL
REMARK 3 B33 (A**2) : NULL
REMARK 3 B12 (A**2) : NULL
REMARK 3 B13 (A**2) : NULL
REMARK 3 B23 (A**2) : NULL
REMARK 3
REMARK 3 ESTIMATED COORDINATE ERROR.
REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.01
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) : 0.014
REMARK 3 BOND ANGLES (DEGREES) : 3.000
REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL
REMARK 3 IMPROPER ANGLES (DEGREES) : NULL
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 : NULL
REMARK 3 TOPOLOGY FILE 1 : NULL
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 1HPX 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_1000173964.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : NULL
REMARK 200 TEMPERATURE (KELVIN) : NULL
REMARK 200 PH : NULL
REMARK 200 NUMBER OF CRYSTALS USED : NULL
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : N
REMARK 200 RADIATION SOURCE : NULL
REMARK 200 BEAMLINE : NULL
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : NULL
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : IMAGE PLATE
REMARK 200 DETECTOR MANUFACTURER : RIGAKU
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MSI
REMARK 200 DATA SCALING SOFTWARE : NULL
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9665
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000
REMARK 200 RESOLUTION RANGE LOW (A) : NULL
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 86.0
REMARK 200 DATA REDUNDANCY : 3.600
REMARK 200 R MERGE (I) : 0.06500
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> 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 <I/SIGMA(I)> FOR SHELL : NULL
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: NULL
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL
REMARK 200 SOFTWARE USED: X-PLOR
REMARK 200 STARTING MODEL: NULL
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 44.34
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.21
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: NULL
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 25.95000
REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 31.15000
REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 29.55000
REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 31.15000
REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 25.95000
REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 29.55000
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: DIMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 4970 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 9180 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -28.0 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: 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 ARG A 57 NE - CZ - NH2 ANGL. DEV. = -3.8 DEGREES
REMARK 500 TYR B 59 CB - CG - CD2 ANGL. DEV. = -4.0 DEGREES
REMARK 500
REMARK 500 REMARK: NULL
REMARK 630
REMARK 630 MOLECULE TYPE: PEPTIDE-LIKE ENZYME INHIBITOR
REMARK 630 MOLECULE NAME: (4R)-N-TERT-BUTYL-3-[(2S,3S)-2-HYDROXY-3-({N-
REMARK 630 [(ISOQUINOLIN-5-YLOXY)ACETYL]-S-METHYL-L-CYSTEINYL}AMINO)-4-
REMARK 630 PHENYLBUTANOYL]-1,3-THIAZOLIDINE-4-CARBOXAMIDE
REMARK 630 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 630 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.)
REMARK 630
REMARK 630 M RES C SSSEQI
REMARK 630 KNI B 900
REMARK 630 SOURCE: NULL
REMARK 630 TAXONOMY: NULL
REMARK 630 SUBCOMP: TUC SMC 005 PRS NTB
REMARK 630 DETAILS: NULL
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE KNI B 900
DBREF 1HPX A 1 99 UNP P03367 POL_HV1BR 69 167
DBREF 1HPX B 1 99 UNP P03367 POL_HV1BR 69 167
SEQRES 1 A 99 PRO GLN ILE 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 CYS THR LEU ASN PHE
SEQRES 1 B 99 PRO GLN ILE 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 CYS THR LEU ASN PHE
HET KNI B 900 87
HETNAM KNI (4R)-N-TERT-BUTYL-3-[(2S,3S)-2-HYDROXY-3-({N-
HETNAM 2 KNI [(ISOQUINOLIN-5-YLOXY)ACETYL]-S-METHYL-L-
HETNAM 3 KNI CYSTEINYL}AMINO)-4-PHENYLBUTANOYL]-1,3-THIAZOLIDINE-4-
HETNAM 4 KNI CARBOXAMIDE
HETSYN KNI KNI-272; (N-TERT-BUTYL-THIOPROLINE)-(5-
HETSYN 2 KNI ISOQUINOLYLOXYACETYL-METHYLTHIOALANINE)-
HETSYN 3 KNI ALLOPHENYLNORSTATINE
FORMUL 3 KNI C33 H41 N5 O6 S2
FORMUL 4 HOH *6(H2 O)
HELIX 1 1 ARG A 87 ILE A 93 1 7
HELIX 2 2 ARG B 87 LEU B 90 1 4
SHEET 1 A 2 LEU A 10 ILE A 15 0
SHEET 2 A 2 GLN A 18 LEU A 23 -1 N ALA A 22 O VAL A 11
SHEET 1 B 4 THR A 31 GLU A 34 0
SHEET 2 B 4 VAL A 75 GLY A 78 1 N LEU A 76 O THR A 31
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 ILE A 62 ILE A 66 0
SHEET 2 C 2 HIS A 69 GLY A 73 -1 N GLY A 73 O ILE A 62
SHEET 1 D 2 THR A 96 ASN A 98 0
SHEET 2 D 2 THR B 96 ASN B 98 -1 N ASN B 98 O THR A 96
SHEET 1 E 4 GLN B 18 LEU B 23 0
SHEET 2 E 4 LEU B 10 ILE B 15 -1 N ILE B 15 O GLN B 18
SHEET 3 E 4 ILE B 62 ILE B 66 -1 N GLU B 65 O LYS B 14
SHEET 4 E 4 HIS B 69 GLY B 73 -1 N GLY B 73 O ILE B 62
SHEET 1 F 3 TRP B 42 GLY B 49 0
SHEET 2 F 3 GLY B 52 TYR B 59 -1 N GLN B 58 O LYS B 43
SHEET 3 F 3 VAL B 75 GLY B 78 -1 N VAL B 77 O ARG B 57
SITE 1 AC1 17 ASP A 25 GLY A 27 ALA A 28 PRO A 81
SITE 2 AC1 17 VAL A 82 ILE A 84 ASP B 25 GLY B 27
SITE 3 AC1 17 ALA B 28 ASP B 29 ASP B 30 GLY B 48
SITE 4 AC1 17 GLY B 49 ILE B 50 HOH B 301 HOH B 566
SITE 5 AC1 17 HOH B 608
CRYST1 51.900 59.100 62.300 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 0.019268 0.000000 0.000000 0.00000
SCALE2 0.000000 0.016920 0.000000 0.00000
SCALE3 0.000000 0.000000 0.016051 0.00000