HEADER HYDROLASE 04-OCT-99 1D4J TITLE HIV-1 PROTEASE IN COMPLEX WITH THE INHIBITOR MSL370 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 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HUMAN IMMUNODEFICIENCY VIRUS; SOURCE 3 ORGANISM_TAXID: 12721; SOURCE 4 STRAIN: BH10; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PET11C KEYWDS DIMER, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR T.UNGE REVDAT 3 24-FEB-09 1D4J 1 VERSN REVDAT 2 05-APR-05 1D4J 1 JRNL REVDAT 1 26-JUN-02 1D4J 0 JRNL AUTH H.O.ANDERSSON,K.FRIDBORG,S.LOWGREN,M.ALTERMAN, JRNL AUTH 2 A.MUHLMAN,M.BJORSNE,N.GARG,I.KVARNSTROM,W.SCHAAL, JRNL AUTH 3 B.CLASSON,U.H.DANIELSSON,G.AHLSEN,U.NILLROTH, JRNL AUTH 4 L.VRANG,B.OBERG,B.SAMUELSSON,A.HALLBERG,T.UNGE JRNL TITL OPTIMIZATION OF P1-P3 GROUPS IN SYMMETRIC AND JRNL TITL 2 ASYMMETRIC HIV-1 PROTEASE INHIBITORS. JRNL REF EUR.J.BIOCHEM. V. 270 1746 2003 JRNL REFN ISSN 0014-2956 JRNL PMID 12694187 JRNL DOI 10.1046/J.1432-1033.2003.03533.X REMARK 1 REMARK 2 REMARK 2 RESOLUTION. 1.81 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 0.9 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES, PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.81 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 14.99 REMARK 3 DATA CUTOFF (SIGMA(F)) : 1.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1192522.560 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 97.2 REMARK 3 NUMBER OF REFLECTIONS : 21687 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) : 0.199 REMARK 3 FREE R VALUE : 0.229 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1116 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.007 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.81 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.92 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 93.70 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 3240 REMARK 3 BIN R VALUE (WORKING SET) : 0.2470 REMARK 3 BIN FREE R VALUE : 0.2740 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.50 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 190 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.020 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 : 47 REMARK 3 SOLVENT ATOMS : 92 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 16.90 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.30 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 4.59000 REMARK 3 B22 (A**2) : -3.32000 REMARK 3 B33 (A**2) : -1.27000 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) : 0.22 REMARK 3 ESD FROM SIGMAA (A) : 0.14 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.25 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.18 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.20 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 25.20 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.85 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 0.720 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.260 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 1.110 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 1.770 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.38 REMARK 3 BSOL : 44.41 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 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : MSL370.PAR REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : MSL370.TOP REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REFINED WITH CNS PROGRAM SYSTEM REMARK 4 REMARK 4 1D4J COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-OCT-99. REMARK 100 THE RCSB ID CODE IS RCSB009783. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-OCT-98 REMARK 200 TEMPERATURE (KELVIN) : 277.0 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 8 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : LURE REMARK 200 BEAMLINE : D41A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.375 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21687 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.810 REMARK 200 RESOLUTION RANGE LOW (A) : 14.990 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.2 REMARK 200 DATA REDUNDANCY : 4.400 REMARK 200 R MERGE (I) : 0.08700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.81 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.92 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.7 REMARK 200 DATA REDUNDANCY IN SHELL : 4.40 REMARK 200 R MERGE FOR SHELL (I) : 0.24700 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: CNS REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.12 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.74 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: SODIUM CHLORIDE, MES, PH 5.5, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 277K 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 29.38950 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 43.26150 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 29.38950 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 43.26150 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 REMARK 300 DIMER. 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: 5110 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9350 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -39.0 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: 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 A 79 53.55 -69.62 REMARK 500 GLU B 135 127.68 -38.57 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 RESIDUE MSC B 501 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1AJV RELATED DB: PDB REMARK 900 SAME PROTEIN COMPLEXED WITH THE CYCLIC SULFAMIDE INHIBITOR REMARK 900 AHA006 REMARK 900 RELATED ID: 1AJX RELATED DB: PDB REMARK 900 SAME PROTEIN COMPLEXED WITH THE CYCLIC UREA INHIBITOR AHA001 REMARK 900 RELATED ID: 1D4H RELATED DB: PDB REMARK 900 SAME PROTEIN COMPLEXED WITH BEA435 REMARK 900 RELATED ID: 1D4I RELATED DB: PDB REMARK 900 SAME PROTEIN COMPLEXED WITH BEA425 REMARK 900 RELATED ID: 1D4J RELATED DB: PDB REMARK 900 SAME PROTEIN COMPLEXED WITH MSL370 DBREF 1D4J A 1 99 UNP P03366 POL_HV1B1 69 167 DBREF 1D4J B 101 199 UNP P03366 POL_HV1B1 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 MSC B 501 47 HETNAM MSC 2,5-DIBENZYLOXY-3,4-DIHYDROXY-HEXANEDIOIC ACID 2- HETNAM 2 MSC CHLORO-6-FLUORO-BENZYLAMIDE (2-HYDROXY-INDAN-1- YL)- HETNAM 3 MSC AMIDE HETSYN MSC INHIBITOR MSL370 FORMUL 3 MSC C36 H36 CL F N2 O7 FORMUL 4 HOH *92(H2 O) HELIX 1 1 GLY A 86 THR A 91 1 6 HELIX 2 2 GLN A 92 GLY A 94 5 3 HELIX 3 3 GLY B 186 THR B 191 1 6 SHEET 1 A 4 GLN A 2 ILE A 3 0 SHEET 2 A 4 THR B 196 ASN B 198 -1 O LEU B 197 N ILE A 3 SHEET 3 A 4 THR A 96 ASN A 98 -1 N THR A 96 O ASN B 198 SHEET 4 A 4 GLN B 102 ILE B 103 -1 N ILE B 103 O LEU A 97 SHEET 1 B 8 LYS A 43 GLY A 49 0 SHEET 2 B 8 GLY A 52 ILE A 66 -1 O GLY A 52 N GLY A 49 SHEET 3 B 8 HIS A 69 VAL A 77 -1 O HIS A 69 N ILE A 66 SHEET 4 B 8 THR A 31 LEU A 33 1 O THR A 31 N LEU A 76 SHEET 5 B 8 ILE A 84 ILE A 85 -1 N ILE A 84 O VAL A 32 SHEET 6 B 8 GLN A 18 LEU A 24 1 O LEU A 23 N ILE A 85 SHEET 7 B 8 LEU A 10 ILE A 15 -1 O VAL A 11 N ALA A 22 SHEET 8 B 8 GLY A 52 ILE A 66 -1 N GLU A 65 O LYS A 14 SHEET 1 C 8 LYS B 143 GLY B 148 0 SHEET 2 C 8 PHE B 153 ILE B 166 -1 O ILE B 154 N ILE B 147 SHEET 3 C 8 LEU B 110 ILE B 115 -1 O LYS B 114 N GLU B 165 SHEET 4 C 8 GLN B 118 LEU B 124 -1 O GLN B 118 N ILE B 115 SHEET 5 C 8 ILE B 184 ILE B 185 1 N ILE B 185 O LEU B 123 SHEET 6 C 8 VAL B 132 LEU B 133 -1 O VAL B 132 N ILE B 184 SHEET 7 C 8 HIS B 169 VAL B 177 1 O LEU B 176 N LEU B 133 SHEET 8 C 8 PHE B 153 ILE B 166 -1 N ARG B 157 O VAL B 177 SITE 1 AC1 24 ARG A 8 LEU A 23 ASP A 25 GLY A 27 SITE 2 AC1 24 ALA A 28 ASP A 30 GLY A 48 GLY A 49 SITE 3 AC1 24 VAL A 82 ILE A 84 HOH A 301 HOH A 318 SITE 4 AC1 24 ARG B 108 LEU B 123 ASP B 125 GLY B 127 SITE 5 AC1 24 ALA B 128 ASP B 129 ASP B 130 GLY B 148 SITE 6 AC1 24 GLY B 149 PRO B 181 VAL B 182 HOH B 304 CRYST1 58.779 86.523 46.575 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 0.017013 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011558 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021471 0.00000 MASTER 259 0 1 3 20 0 6 6 0 0 0 16 END