HEADER HYDROLASE/HYDROLASE INHIBITOR 25-JUL-00 1FG6
TITLE STRUCTURAL IMPLICATIONS OF DRUG RESISTANT MUTANTS OF HIV-1 PROTEASE:
TITLE 2 HIGH RESOLUTION CRYSTAL STRUCTURES OF THE MUTANT PROTEASE/SUBSTRATE
TITLE 3 ANALOG COMPLEXES
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: PROTEASE RETROPEPSIN;
COMPND 3 CHAIN: C, D;
COMPND 4 EC: 3.4.23.16;
COMPND 5 ENGINEERED: YES;
COMPND 6 MUTATION: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: HUMAN IMMUNODEFICIENCY VIRUS 1;
SOURCE 3 ORGANISM_TAXID: 11676;
SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562
KEYWDS HIV-1 PROTEASE, HYDROLASE-HYDROLASE INHIBITOR COMPLEX
EXPDTA X-RAY DIFFRACTION
AUTHOR B.MAHALINGAM,J.M.LOUIS,R.W.HARRISON,I.T.WEBER
REVDAT 7 13-MAR-24 1FG6 1 COMPND SOURCE
REVDAT 6 07-FEB-24 1FG6 1 REMARK
REVDAT 5 03-NOV-21 1FG6 1 REMARK SEQADV
REVDAT 4 09-MAY-12 1FG6 1 CAVEAT REMARK
REVDAT 3 13-JUL-11 1FG6 1 VERSN
REVDAT 2 24-FEB-09 1FG6 1 VERSN
REVDAT 1 01-JUN-01 1FG6 0
JRNL AUTH B.MAHALINGAM,J.M.LOUIS,J.HUNG,R.W.HARRISON,I.T.WEBER
JRNL TITL STRUCTURAL IMPLICATIONS OF DRUG-RESISTANT MUTANTS OF HIV-1
JRNL TITL 2 PROTEASE: HIGH-RESOLUTION CRYSTAL STRUCTURES OF THE MUTANT
JRNL TITL 3 PROTEASE/SUBSTRATE ANALOGUE COMPLEXES.
JRNL REF PROTEINS V. 43 455 2001
JRNL REFN ISSN 0887-3585
JRNL PMID 11340661
JRNL DOI 10.1002/PROT.1057
REMARK 2
REMARK 2 RESOLUTION. 1.80 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : X-PLOR 3.843
REMARK 3 AUTHORS : BRUNGER
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.00
REMARK 3 DATA CUTOFF (SIGMA(F)) : 1.000
REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL
REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL
REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL
REMARK 3 NUMBER OF REFLECTIONS : NULL
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) : 0.219
REMARK 3 FREE R VALUE : 0.248
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.900
REMARK 3 FREE R VALUE TEST SET COUNT : 1190
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 : 1512
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 54
REMARK 3 SOLVENT ATOMS : 111
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) : 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) : NULL
REMARK 3 BOND ANGLES (DEGREES) : NULL
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 1FG6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-AUG-00.
REMARK 100 THE DEPOSITION ID IS D_1000011563.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 09-OCT-99
REMARK 200 TEMPERATURE (KELVIN) : 90
REMARK 200 PH : NULL
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : NSLS
REMARK 200 BEAMLINE : X12B
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 1.037
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO
REMARK 200 DATA SCALING SOFTWARE : SCALEPACK
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800
REMARK 200 RESOLUTION RANGE LOW (A) : 25.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : NULL
REMARK 200 DATA REDUNDANCY : NULL
REMARK 200 R MERGE (I) : 0.06800
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) : 1.80
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.88
REMARK 200 COMPLETENESS FOR SHELL (%) : 90.1
REMARK 200 DATA REDUNDANCY IN SHELL : NULL
REMARK 200 R MERGE FOR SHELL (I) : 0.31300
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: NULL
REMARK 200 SOFTWARE USED: AMORE
REMARK 200 STARTING MODEL: NULL
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 51.56
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.54
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: CITRATE/PHOSPHATE BUFFER 0.05M, DTT
REMARK 280 10MM, DMSO 10%, SATURATED AMMONIUM SULPHAT25-50%, PROTEIN 2-5 MG/
REMARK 280 ML, PH 5.0-6.5. VAPOR DIFFUSION, HANGING DROP AT 298K
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 28.65750
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 42.71350
REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000
REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 28.65750
REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 42.71350
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 300 REMARK: THE BIOLOGICAL ASSEMBLY IS A DIMER CONSISTING OF CHAINS C
REMARK 300 AND D
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: 5490 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 9180 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -30.0 KCAL/MOL
REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D
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 600
REMARK 600 HETEROGEN
REMARK 600
REMARK 600 THE INHIBITOR 2NC HAS A REDUCED PEPTIDE BOND ISOSTERE [CH2-NH] IN
REMARK 600 PLACE OF THE SCISSILE AMIDE. THE COORDINATES OF 2NC WERE DEPOSITED
REMARK 600 WITH AN EXTRA ATOM O6 AT ZERO OCCUPANCY. THIS ZERO OCCUPANCY O6 HAS
REMARK 600 BEEN REMOVED FROM THE RELEASED FILE.
REMARK 630
REMARK 630 MOLECULE TYPE: PEPTIDE-LIKE INHIBITOR
REMARK 630 MOLECULE NAME: N-{(2S)-2-[(N-ACETYL-L-THREONYL-L-ISOLEUCYL)AMINO]
REMARK 630 HEXYL}-L-NORLEUCYL-L-GLUTAMINYL-N~5~-[AMINO(IMINIO)METHYL]-L-
REMARK 630 ORNITHINAMIDE
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 2NC D 300
REMARK 630 SOURCE: NULL
REMARK 630 TAXONOMY: NULL
REMARK 630 SUBCOMP: ACE THR ILE 2A0 GLN ARG NH2
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 2NC D 300
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 1A94 RELATED DB: PDB
REMARK 900 RELATED ID: 1DAZ RELATED DB: PDB
REMARK 999
REMARK 999 SEQUENCE
REMARK 999 MUTATIONS Q7K, L33I, L63I, C67A, C95A, HAVE BEEN MADE TO
REMARK 999 STABILIZE THE PROTEASE FROM AUTOPROTEOLYSIS, WHILE
REMARK 999 RETAINING ACTIVITY SIMILAR TO WILD-TYPE HIV-1 PROTEASE
DBREF 1FG6 C 1 99 UNP P04587 POL_HV1B5 69 167
DBREF 1FG6 D 101 199 UNP P04587 POL_HV1B5 69 167
SEQADV 1FG6 LYS C 7 UNP P04587 GLN 75 ENGINEERED MUTATION
SEQADV 1FG6 ILE C 33 UNP P04587 LEU 101 ENGINEERED MUTATION
SEQADV 1FG6 ILE C 63 UNP P04587 LEU 131 ENGINEERED MUTATION
SEQADV 1FG6 ALA C 67 UNP P04587 CYS 135 ENGINEERED MUTATION
SEQADV 1FG6 ASP C 88 UNP P04587 ASN 156 ENGINEERED MUTATION
SEQADV 1FG6 ALA C 95 UNP P04587 CYS 163 ENGINEERED MUTATION
SEQADV 1FG6 LYS D 107 UNP P04587 GLN 75 ENGINEERED MUTATION
SEQADV 1FG6 ILE D 133 UNP P04587 LEU 101 ENGINEERED MUTATION
SEQADV 1FG6 ILE D 163 UNP P04587 LEU 131 ENGINEERED MUTATION
SEQADV 1FG6 ALA D 167 UNP P04587 CYS 135 ENGINEERED MUTATION
SEQADV 1FG6 ASP D 188 UNP P04587 ASN 156 ENGINEERED MUTATION
SEQADV 1FG6 ALA D 195 UNP P04587 CYS 163 ENGINEERED MUTATION
SEQRES 1 C 99 PRO GLN ILE THR LEU TRP LYS ARG PRO LEU VAL THR ILE
SEQRES 2 C 99 LYS ILE GLY GLY GLN LEU LYS GLU ALA LEU LEU ASP THR
SEQRES 3 C 99 GLY ALA ASP ASP THR VAL ILE GLU GLU MET SER LEU PRO
SEQRES 4 C 99 GLY ARG TRP LYS PRO LYS MET ILE GLY GLY ILE GLY GLY
SEQRES 5 C 99 PHE ILE LYS VAL ARG GLN TYR ASP GLN ILE ILE ILE GLU
SEQRES 6 C 99 ILE ALA GLY HIS LYS ALA ILE GLY THR VAL LEU VAL GLY
SEQRES 7 C 99 PRO THR PRO VAL ASN ILE ILE GLY ARG ASP LEU LEU THR
SEQRES 8 C 99 GLN ILE GLY ALA THR LEU ASN PHE
SEQRES 1 D 99 PRO GLN ILE THR LEU TRP LYS ARG PRO LEU VAL THR ILE
SEQRES 2 D 99 LYS ILE GLY GLY GLN LEU LYS GLU ALA LEU LEU ASP THR
SEQRES 3 D 99 GLY ALA ASP ASP THR VAL ILE GLU GLU MET SER LEU PRO
SEQRES 4 D 99 GLY ARG TRP LYS PRO LYS MET ILE GLY GLY ILE GLY GLY
SEQRES 5 D 99 PHE ILE LYS VAL ARG GLN TYR ASP GLN ILE ILE ILE GLU
SEQRES 6 D 99 ILE ALA GLY HIS LYS ALA ILE GLY THR VAL LEU VAL GLY
SEQRES 7 D 99 PRO THR PRO VAL ASN ILE ILE GLY ARG ASP LEU LEU THR
SEQRES 8 D 99 GLN ILE GLY ALA THR LEU ASN PHE
HET 2NC D 300 54
HETNAM 2NC N-{(2S)-2-[(N-ACETYL-L-THREONYL-L-ISOLEUCYL)
HETNAM 2 2NC AMINO]HEXYL}-L-NORLEUCYL-L-GLUTAMINYL-N~5~-
HETNAM 3 2NC [AMINO(IMINIO)METHYL]-L-ORNITHINAMIDE
HETSYN 2NC P2/NC
FORMUL 3 2NC C35 H68 N11 O8 1+
FORMUL 4 HOH *111(H2 O)
HELIX 1 1 GLY C 86 THR C 91 1 6
HELIX 2 2 GLY D 186 ILE D 193 1 8
SHEET 1 A 4 GLN C 2 THR C 4 0
SHEET 2 A 4 THR D 196 ASN D 198 -1 O LEU D 197 N ILE C 3
SHEET 3 A 4 THR C 96 ASN C 98 -1 O THR C 96 N ASN D 198
SHEET 4 A 4 GLN D 102 THR D 104 -1 N ILE D 103 O LEU C 97
SITE 1 AC1 26 LEU C 23 ASP C 25 GLY C 27 ALA C 28
SITE 2 AC1 26 ASP C 29 ASP C 30 GLY C 48 GLY C 49
SITE 3 AC1 26 VAL C 82 ILE C 84 HOH C 101 HOH D 19
SITE 4 AC1 26 HOH D 39 HOH D 62 ASP D 125 GLY D 127
SITE 5 AC1 26 ALA D 128 ASP D 129 ASP D 130 ILE D 147
SITE 6 AC1 26 GLY D 148 GLY D 149 VAL D 182 HOH D 205
SITE 7 AC1 26 HOH D 240 HOH D 257
CRYST1 57.315 85.427 46.186 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 0.017447 0.000000 0.000000 0.00000
SCALE2 0.000000 0.011706 0.000000 0.00000
SCALE3 0.000000 0.000000 0.021652 0.00000