HEADER HYDROLASE/HYDROLASE INHIBITOR 25-JUL-00 1FFI 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 1FFI 1 COMPND SOURCE REVDAT 6 07-FEB-24 1FFI 1 REMARK REVDAT 5 03-NOV-21 1FFI 1 REMARK SEQADV REVDAT 4 09-MAY-12 1FFI 1 CAVEAT REMARK REVDAT 3 13-JUL-11 1FFI 1 VERSN REVDAT 2 24-FEB-09 1FFI 1 VERSN REVDAT 1 01-JUN-01 1FFI 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. 1.70 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) : 1.70 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) : 0.211 REMARK 3 FREE R VALUE : 0.252 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.800 REMARK 3 FREE R VALUE TEST SET COUNT : 1485 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 : 117 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 1FFI 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_1000011540. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-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) : 1.700 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) : 0.05900 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) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.78 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.28900 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 (%): 52.15 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.57 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 5-6.5. 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 28.88150 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 42.78450 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 28.88150 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 42.78450 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: 8930 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 1FFI C 1 99 UNP P04587 POL_HV1B5 69 167 DBREF 1FFI D 101 199 UNP P04587 POL_HV1B5 69 167 SEQADV 1FFI LYS C 7 UNP P04587 GLN 75 ENGINEERED MUTATION SEQADV 1FFI ASN C 30 UNP P04587 ASP 98 ENGINEERED MUTATION SEQADV 1FFI ILE C 33 UNP P04587 LEU 101 ENGINEERED MUTATION SEQADV 1FFI ILE C 63 UNP P04587 LEU 131 ENGINEERED MUTATION SEQADV 1FFI ALA C 67 UNP P04587 CYS 135 ENGINEERED MUTATION SEQADV 1FFI ALA C 95 UNP P04587 CYS 163 ENGINEERED MUTATION SEQADV 1FFI LYS D 107 UNP P04587 GLN 75 ENGINEERED MUTATION SEQADV 1FFI ASN D 130 UNP P04587 ASP 98 ENGINEERED MUTATION SEQADV 1FFI ILE D 133 UNP P04587 LEU 101 ENGINEERED MUTATION SEQADV 1FFI ILE D 163 UNP P04587 LEU 131 ENGINEERED MUTATION SEQADV 1FFI ALA D 167 UNP P04587 CYS 135 ENGINEERED MUTATION SEQADV 1FFI 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 ASN 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 ASN 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 ASN 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 ASN 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 *117(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 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 ILE D 103 -1 N ILE D 103 O LEU C 97 SITE 1 AC1 28 ASP C 25 GLY C 27 ALA C 28 ASP C 29 SITE 2 AC1 28 ASN C 30 GLY C 48 GLY C 49 PRO C 81 SITE 3 AC1 28 ILE C 84 HOH D 10 HOH D 17 HOH D 77 SITE 4 AC1 28 HOH D 80 ARG D 108 ASP D 125 GLY D 127 SITE 5 AC1 28 ALA D 128 ASP D 129 ASN D 130 ILE D 147 SITE 6 AC1 28 GLY D 148 GLY D 149 PHE D 153 PRO D 181 SITE 7 AC1 28 VAL D 182 HOH D 203 HOH D 255 HOH D 256 CRYST1 57.763 85.569 46.310 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 0.017312 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011686 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021594 0.00000