HEADER HYDROLASE/HYDROLASE INHIBITOR 25-JUL-00 1FG8 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 6 13-MAR-24 1FG8 1 COMPND SOURCE REVDAT 5 07-FEB-24 1FG8 1 REMARK REVDAT 4 03-NOV-21 1FG8 1 REMARK SEQADV REVDAT 3 13-JUL-11 1FG8 1 VERSN REVDAT 2 24-FEB-09 1FG8 1 VERSN REVDAT 1 01-JUN-01 1FG8 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. 1.85 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) : 1.85 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) : 0.223 REMARK 3 FREE R VALUE : 0.267 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.900 REMARK 3 FREE R VALUE TEST SET COUNT : 941 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 : 59 REMARK 3 SOLVENT ATOMS : 81 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 1FG8 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_1000011565. 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) : 1.850 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) : 0.06400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.85 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.93 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.24100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 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 (%): 39.69 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.04 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 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 25.62050 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 30.48600 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 29.15250 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 30.48600 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 25.62050 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 29.15250 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: 5480 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9040 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -28.0 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 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 C 79 56.84 -67.58 REMARK 500 REMARK 500 REMARK: NULL REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 PEPTIDE INHIBITOR 0Q4 HAS A REDUCED PEPTIDE (-CH2-NH) INSTEAD REMARK 600 OF THE NORMAL PEPTIDE LINK (-CO-NH). REMARK 630 REMARK 630 MOLECULE TYPE: PEPTIDE-LIKE INHIBITOR REMARK 630 MOLECULE NAME: N-[(2R)-2-({N~5~-[AMINO(IMINIO)METHYL]-L-ORNITHYL-L- REMARK 630 VALYL}AMINO)-4-METHYLPENTYL]-L-PHENYLALANYL-L-ALPHA-GLUTAMYL-L- REMARK 630 ALANYL-L-NORLEUCINAMIDE 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 0Q4 C 401 REMARK 630 SOURCE: NULL REMARK 630 TAXONOMY: NULL REMARK 630 SUBCOMP: ARG VAL DC0 GLU ALA NLE 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 0Q4 C 401 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 1FG8 C 1 99 UNP P04587 POL_HV1B5 69 167 DBREF 1FG8 D 101 199 UNP P04587 POL_HV1B5 69 167 SEQADV 1FG8 LYS C 7 UNP P04587 GLN 75 ENGINEERED MUTATION SEQADV 1FG8 ILE C 33 UNP P04587 LEU 101 ENGINEERED MUTATION SEQADV 1FG8 ILE C 63 UNP P04587 LEU 131 ENGINEERED MUTATION SEQADV 1FG8 ALA C 67 UNP P04587 CYS 135 ENGINEERED MUTATION SEQADV 1FG8 ASP C 88 UNP P04587 ASN 156 ENGINEERED MUTATION SEQADV 1FG8 ALA C 95 UNP P04587 CYS 163 ENGINEERED MUTATION SEQADV 1FG8 LYS D 107 UNP P04587 GLN 75 ENGINEERED MUTATION SEQADV 1FG8 ILE D 133 UNP P04587 LEU 101 ENGINEERED MUTATION SEQADV 1FG8 ILE D 163 UNP P04587 LEU 131 ENGINEERED MUTATION SEQADV 1FG8 ALA D 167 UNP P04587 CYS 135 ENGINEERED MUTATION SEQADV 1FG8 ASP D 188 UNP P04587 ASN 156 ENGINEERED MUTATION SEQADV 1FG8 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 0Q4 C 401 118 HETNAM 0Q4 N-[(2R)-2-({N~5~-[AMINO(IMINIO)METHYL]-L-ORNITHYL-L- HETNAM 2 0Q4 VALYL}AMINO)-4-METHYLPENTYL]-L-PHENYLALANYL-L-ALPHA- HETNAM 3 0Q4 GLUTAMYL-L-ALANYL-L-NORLEUCINAMIDE HETSYN 0Q4 INHIBITOR ANALOGUES OF CA-P2 FORMUL 3 0Q4 C40 H70 N11 O8 1+ FORMUL 4 HOH *81(H2 O) HELIX 1 1 GLY C 86 THR C 91 1 6 HELIX 2 2 GLY D 186 THR D 191 1 6 SHEET 1 A 4 GLN C 2 ILE C 3 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 N THR C 96 O 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 38 TRP C 6 ARG C 8 LEU C 23 ASP C 25 SITE 2 AC1 38 GLY C 27 ALA C 28 ASP C 29 ASP C 30 SITE 3 AC1 38 VAL C 32 LYS C 45 MET C 46 ILE C 47 SITE 4 AC1 38 GLY C 48 GLY C 49 ILE C 50 PRO C 81 SITE 5 AC1 38 ILE C 84 HOH C 138 HOH C 177 ARG D 108 SITE 6 AC1 38 LEU D 123 ASP D 125 GLY D 127 ALA D 128 SITE 7 AC1 38 ASP D 129 ASP D 130 VAL D 132 LYS D 145 SITE 8 AC1 38 MET D 146 ILE D 147 GLY D 148 GLY D 149 SITE 9 AC1 38 ILE D 150 GLN D 158 PRO D 181 VAL D 182 SITE 10 AC1 38 ILE D 184 HOH D 201 CRYST1 51.241 58.305 60.972 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 0.019516 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017151 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016401 0.00000