HEADER HYDROLASE 17-OCT-05 2BBB TITLE STRUCTURE OF HIV1 PROTEASE AND HH1_173_3A COMPLEX. COMPND MOL_ID: 1; COMPND 2 MOLECULE: 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 1; SOURCE 3 ORGANISM_TAXID: 11676; SOURCE 4 GENE: GAG; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_VECTOR: PET-3B-HIVPR KEYWDS PROTEASE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR A.B.SMITH III,A.K.CHARNLEY,L.C.KUO,S.MUNSHI REVDAT 4 23-AUG-23 2BBB 1 REMARK REVDAT 3 24-FEB-09 2BBB 1 VERSN REVDAT 2 24-JAN-06 2BBB 1 JRNL REVDAT 1 15-NOV-05 2BBB 0 JRNL AUTH A.B.SMITH III,A.K.CHARNLEY,H.HARADA,J.J.BEIGER,L.D.CANTIN, JRNL AUTH 2 C.S.KENESKY,R.HIRSCHMANN,S.MUNSHI,D.B.OLSEN,M.W.STAHLHUT, JRNL AUTH 3 W.A.SCHLEIF,L.C.KUO JRNL TITL DESIGN, SYNTHESIS, AND BIOLOGICAL EVALUATION OF JRNL TITL 2 MONOPYRROLINONE-BASED HIV-1 PROTEASE INHIBITORS POSSESSING JRNL TITL 3 AUGMENTED P2' SIDE CHAINS JRNL REF BIOORG.MED.CHEM.LETT. V. 16 859 2006 JRNL REFN ISSN 0960-894X JRNL PMID 16298527 JRNL DOI 10.1016/J.BMCL.2005.11.011 REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNX 2000.1 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN,MOLECULAR REMARK 3 : SIMULATIONS (BADGER,BERARD,KUMAR,SZALMA, REMARK 3 : YIP,DZAKULA) REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 6.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 541701.850 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 97.0 REMARK 3 NUMBER OF REFLECTIONS : 24532 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 + TEST SET) : 0.217 REMARK 3 R VALUE (WORKING SET) : 0.217 REMARK 3 FREE R VALUE : 0.229 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.800 REMARK 3 FREE R VALUE TEST SET COUNT : 2415 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.005 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL WITH ALL DATA. REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : NULL REMARK 3 FREE R VALUE (NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL REMARK 3 ESTIMATED ERROR OF FREE R VALUE (NO CUTOFF) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : NULL 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) : 1.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.80 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 91.40 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 3432 REMARK 3 BIN R VALUE (WORKING SET) : 0.3440 REMARK 3 BIN FREE R VALUE : 0.3370 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 9.60 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 365 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.018 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1515 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 46 REMARK 3 SOLVENT ATOMS : 223 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 21.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.80 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.33000 REMARK 3 B22 (A**2) : -2.61000 REMARK 3 B33 (A**2) : 1.29000 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) : 0.21 REMARK 3 ESD FROM SIGMAA (A) : 0.13 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) : 0.23 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.16 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.700 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 25.60 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.800 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) : 1.090 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.680 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.030 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.030 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : 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 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : HH1_173_3A_INHIB.XPRM REMARK 3 PARAMETER FILE 3 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2BBB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-OCT-05. REMARK 100 THE DEPOSITION ID IS D_1000034903. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-JAN-05 REMARK 200 TEMPERATURE (KELVIN) : 93 REMARK 200 PH : 5.2 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25929 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 7.200 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06100 REMARK 200 FOR THE DATA SET : 29.9000 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) : 1.76 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.3 REMARK 200 DATA REDUNDANCY IN SHELL : 6.00 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.67900 REMARK 200 FOR SHELL : 2.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNX 2000.1 REMARK 200 STARTING MODEL: PDB ENTRY: 1NPW REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.49 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.64 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 600 MM NACL, 100MM SODIUM ACETATE, PH REMARK 280 5.2, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 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 28.75450 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 43.10800 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 28.75450 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 43.10800 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: 5010 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9230 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -34.0 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 HH1 A 301 DBREF 2BBB A 1 99 UNP Q5RZ09 Q5RZ09_9HIV1 69 167 DBREF 2BBB B 201 299 UNP Q5RZ09 Q5RZ09_9HIV1 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 HH1 A 301 46 HETNAM HH1 (3S)-TETRAHYDROFURAN-3-YL (1R)-3-{(2R)-4-[(1S,3S)-3-(2- HETNAM 2 HH1 AMINO-2-OXOETHYL)-2,3-DIHYDRO-1H-INDEN-1-YL]-2-BENZYL- HETNAM 3 HH1 3-OXO-2,3-DIHYDRO-1H-PYRROL-2-YL}-1-BENZYL-2- HETNAM 4 HH1 HYDROXYPROPYLCARBAMATE HETSYN HH1 (S)-TETRAHYDROFURAN-3-YL (2S,3S)-4-((S)-4-((1R,3R)-3- HETSYN 2 HH1 (2-AMINO-2-OXOETHYL)-2,3-DIHYDRO-1H-INDEN-1-YL)-2- HETSYN 3 HH1 BENZYL-3-OXO-2,3-DIHYDRO-1H-PYRROL-2-YL)-3-HYDROXY-1- HETSYN 4 HH1 PHENYLBUTAN-2-YLCARBAMATE FORMUL 3 HH1 C37 H41 N3 O6 FORMUL 4 HOH *223(H2 O) HELIX 1 1 GLY A 86 THR A 91 1 6 HELIX 2 2 GLY B 286 THR B 291 1 6 SHEET 1 A 4 GLN A 2 ILE A 3 0 SHEET 2 A 4 THR B 296 ASN B 298 -1 O LEU B 297 N ILE A 3 SHEET 3 A 4 THR A 96 ASN A 98 -1 N ASN A 98 O THR B 296 SHEET 4 A 4 GLN B 202 ILE B 203 -1 O ILE B 203 N LEU A 97 SHEET 1 B 8 TRP A 42 GLY A 49 0 SHEET 2 B 8 GLY A 52 ILE A 66 -1 O VAL A 56 N LYS A 45 SHEET 3 B 8 HIS A 69 VAL A 77 -1 O VAL A 77 N ARG A 57 SHEET 4 B 8 VAL A 32 LEU A 33 1 N LEU A 33 O LEU A 76 SHEET 5 B 8 ILE A 84 ILE A 85 -1 O ILE A 84 N VAL A 32 SHEET 6 B 8 GLN A 18 LEU A 24 1 N LEU A 23 O ILE A 85 SHEET 7 B 8 LEU A 10 ILE A 15 -1 N ILE A 13 O LYS A 20 SHEET 8 B 8 GLY A 52 ILE A 66 -1 O GLU A 65 N LYS A 14 SHEET 1 C 8 LYS B 243 GLY B 249 0 SHEET 2 C 8 GLY B 252 ILE B 266 -1 O GLN B 258 N LYS B 243 SHEET 3 C 8 HIS B 269 VAL B 277 -1 O HIS B 269 N ILE B 266 SHEET 4 C 8 VAL B 232 LEU B 233 1 N LEU B 233 O LEU B 276 SHEET 5 C 8 ILE B 284 ILE B 285 -1 O ILE B 284 N VAL B 232 SHEET 6 C 8 GLN B 218 LEU B 224 1 N LEU B 223 O ILE B 285 SHEET 7 C 8 LEU B 210 ILE B 215 -1 N VAL B 211 O ALA B 222 SHEET 8 C 8 GLY B 252 ILE B 266 -1 O GLU B 265 N LYS B 214 SITE 1 AC1 21 ASP A 25 GLY A 27 ALA A 28 ASP A 29 SITE 2 AC1 21 ASP A 30 VAL A 32 GLY A 48 GLY A 49 SITE 3 AC1 21 HOH A 311 LEU B 223 ASP B 225 GLY B 227 SITE 4 AC1 21 ALA B 228 ASP B 229 ASP B 230 VAL B 232 SITE 5 AC1 21 GLY B 248 GLY B 249 ILE B 250 PRO B 281 SITE 6 AC1 21 ILE B 284 CRYST1 57.509 86.216 46.130 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 0.017389 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011599 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021678 0.00000