PDB Short entry for 1EC2 HEADER HYDROLASE/HYDROLASE INHIBITOR 25-JAN-00 1EC2 TITLE HIV-1 PROTEASE IN COMPLEX WITH THE INHIBITOR BEA428 COMPND MOL_ID: 1; COMPND 2 MOLECULE: HIV-1 PROTEASE; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: FRAGMENT 69-167; COMPND 5 EC: 3.4.23.16; COMPND 6 ENGINEERED: 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; SOURCE 6 EXPRESSION_SYSTEM_PLASMID: PET11C KEYWDS DIMER, PROTEIN-INHIBITOR COMPLEX, HYDROLASE-HYDROLASE INHIBITOR KEYWDS 2 COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR T.UNGE REVDAT 5 07-FEB-24 1EC2 1 REMARK REVDAT 4 07-MAR-18 1EC2 1 REMARK REVDAT 3 24-FEB-09 1EC2 1 VERSN REVDAT 2 29-MAR-05 1EC2 1 JRNL REVDAT 1 26-JUN-02 1EC2 0 JRNL AUTH H.O.ANDERSSON,K.FRIDBORG,S.LOWGREN,M.ALTERMAN,A.MUHLMAN, JRNL AUTH 2 M.BJORSNE,N.GARG,I.KVARNSTROM,W.SCHAAL,B.CLASSON,A.KARLEN, JRNL AUTH 3 U.H.DANIELSSON,G.AHLSEN,U.NILLROTH,L.VRANG,B.OBERG, JRNL AUTH 4 B.SAMUELSSON,A.HALLBERG,T.UNGE JRNL TITL OPTIMIZATION OF P1-P3 GROUPS IN SYMMETRIC AND ASYMMETRIC JRNL TITL 2 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 2 REMARK 2 RESOLUTION. 2.00 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.76 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1356235.780 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 90.5 REMARK 3 NUMBER OF REFLECTIONS : 15012 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) : 0.209 REMARK 3 FREE R VALUE : 0.245 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 753 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.009 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) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.13 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 90.10 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2336 REMARK 3 BIN R VALUE (WORKING SET) : 0.2500 REMARK 3 BIN FREE R VALUE : 0.2490 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.80 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 117 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.023 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 : 56 REMARK 3 SOLVENT ATOMS : 95 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 6.60 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.20 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 3.22000 REMARK 3 B22 (A**2) : -1.09000 REMARK 3 B33 (A**2) : -2.14000 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) : 0.25 REMARK 3 ESD FROM SIGMAA (A) : 0.19 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) : 0.29 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) : 1.300 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 25.30 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.720 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) : 0.830 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.310 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 5.770 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 4.150 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.33 REMARK 3 BSOL : 35.60 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.PA REMARK 3 PARAMETER FILE 2 : WATER_REP.PARA REMARK 3 PARAMETER FILE 3 : BEA428.PAR REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : BEA428.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 1EC2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 31-JAN-00. REMARK 100 THE DEPOSITION ID IS D_1000010445. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-MAR-98 REMARK 200 TEMPERATURE (KELVIN) : 277 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 6 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : MAX II REMARK 200 BEAMLINE : I711 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.958 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 : 15012 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 24.760 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 90.5 REMARK 200 DATA REDUNDANCY : 3.020 REMARK 200 R MERGE (I) : 0.12800 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 6.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.13 REMARK 200 COMPLETENESS FOR SHELL (%) : 90.1 REMARK 200 DATA REDUNDANCY IN SHELL : 1.50 REMARK 200 R MERGE FOR SHELL (I) : 0.39000 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: X-PLOR REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.91 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.73 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.4 M SODIUM CHLORIDE, 0.05 M MES, REMARK 280 0.02 % (W/V) SODIUM AZIDE, PH 5.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 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 29.24000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 43.33500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 29.24000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 43.33500 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 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: 5340 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9090 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 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BEJ B 501 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1AJV RELATED DB: PDB REMARK 900 1AJV CONTAINS THE SAME PROTEIN COMPLEXED WITH THE CYCLIC SULFAMIDE REMARK 900 INHIBITOR AHA006 REMARK 900 RELATED ID: 1AJX RELATED DB: PDB REMARK 900 1AJX CONTAINS THE SAME PROTEIN COMPLEXED WITH THE CYCLIC UREA REMARK 900 INHIBITOR AHA001 REMARK 900 RELATED ID: 1D4I RELATED DB: PDB REMARK 900 D4I CONTAINS THE SAME PROTEIN COMPLEXED WITH THE INHIBITOR BEA425 REMARK 900 RELATED ID: 1D4H RELATED DB: PDB REMARK 900 1D4H CONTAINS THE SAME PROTEIN COMPLEXED WITH THE INHIBITOR BEA435 REMARK 900 RELATED ID: 1D4J RELATED DB: PDB REMARK 900 1D4J CONTAINS THE SAME PROTEIN COMPLEXED WITH THE INHIBITOR MSL370 REMARK 900 RELATED ID: 1EBW RELATED DB: PDB REMARK 900 HIV-1 PROTEASE IN COMPLEX WITH THE INHIBITOR BEA322 REMARK 900 RELATED ID: 1EBY RELATED DB: PDB REMARK 900 HIV-1 PROTEASE IN COMPLEX WITH THE INHIBITOR BEA369 REMARK 900 RELATED ID: 1EBZ RELATED DB: PDB REMARK 900 HIV-1 PROTEASE IN COMPLEX WITH THE INHIBITOR BEA388 REMARK 900 RELATED ID: 1EC0 RELATED DB: PDB REMARK 900 HIV-1 PROTEASE IN COMPLEX WITH THE INHIBITOR BEA403 REMARK 900 RELATED ID: 1EC1 RELATED DB: PDB REMARK 900 HIV-1 PROTEASE IN COMPLEX WITH THE INHIBITOR BEA409 REMARK 900 RELATED ID: 1EC3 RELATED DB: PDB REMARK 900 HIV-1 PROTEASE IN COMPLEX WITH THE INHIBITOR MSA367 DBREF 1EC2 A 1 99 UNP P03366 POL_HV1B1 69 167 DBREF 1EC2 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 BEJ B 501 56 HETNAM BEJ N,N-[2,5-O-[DI-4-PYRIDIN-3-YL-BENZYL]-GLUCARYL]-DI- HETNAM 2 BEJ [VALYL-AMIDO-METHANE] HETSYN BEJ INHIBITOR BEA428 FORMUL 3 BEJ C42 H52 N6 O8 FORMUL 4 HOH *95(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 LEU A 10 ILE A 15 -1 O LYS A 14 N GLU A 65 SHEET 4 B 8 GLN A 18 LEU A 24 -1 O GLN A 18 N ILE A 15 SHEET 5 B 8 ILE A 84 ILE A 85 1 N ILE A 85 O LEU A 23 SHEET 6 B 8 VAL A 32 LEU A 33 -1 O VAL A 32 N ILE A 84 SHEET 7 B 8 HIS A 69 VAL A 77 1 O LEU A 76 N LEU A 33 SHEET 8 B 8 GLY A 52 ILE A 66 -1 N ARG A 57 O VAL A 77 SHEET 1 C 8 LYS B 143 GLY B 149 0 SHEET 2 C 8 GLY B 152 ILE B 166 -1 O GLY B 152 N GLY B 149 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 GLY B 152 ILE B 166 -1 N ARG B 157 O VAL B 177 SITE 1 AC1 20 ARG A 8 ASP A 25 GLY A 27 ALA A 28 SITE 2 AC1 20 ASP A 29 GLY A 48 GLY A 49 PRO A 81 SITE 3 AC1 20 ILE A 84 ARG B 108 ASP B 125 GLY B 127 SITE 4 AC1 20 ALA B 128 ASP B 129 GLY B 148 GLY B 149 SITE 5 AC1 20 VAL B 182 ILE B 184 HOH B 607 HOH B 608 CRYST1 58.480 86.670 46.520 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 0.017100 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011538 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021496 0.00000