PDB Short entry for 2BZ5 HEADER CHAPERONE 11-AUG-05 2BZ5 TITLE STRUCTURE-BASED DISCOVERY OF A NEW CLASS OF HSP90 INHIBITORS COMPND MOL_ID: 1; COMPND 2 MOLECULE: HEAT SHOCK PROTEIN HSP90-ALPHA; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: N-TERMINAL DOMAIN, RESIDUES 1-235; COMPND 5 SYNONYM: HSP 86; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 ORGAN: SKIN; SOURCE 6 TISSUE: MELANOMA; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET19 KEYWDS ATP-BINDING, CHAPERONE, HEAT SHOCK, NUCLEOTIDE-BINDING, KEYWDS 2 PHOSPHORYLATION EXPDTA X-RAY DIFFRACTION AUTHOR X.BARRIL,P.BROUGH,M.DRYSDALE,R.E.HUBBARD,A.MASSEY,A.SURGENOR,L.WRIGHT REVDAT 5 13-DEC-23 2BZ5 1 LINK REVDAT 4 31-JAN-18 2BZ5 1 SOURCE REVDAT 3 24-FEB-09 2BZ5 1 VERSN REVDAT 2 26-OCT-05 2BZ5 1 JRNL REVDAT 1 12-OCT-05 2BZ5 0 JRNL AUTH X.BARRIL,P.BROUGH,M.DRYSDALE,R.E.HUBBARD,A.MASSEY, JRNL AUTH 2 A.SURGENOR,L.WRIGHT JRNL TITL STRUCTURE-BASED DISCOVERY OF A NEW CLASS OF HSP90 JRNL TITL 2 INHIBITORS. JRNL REF BIOORG.MED.CHEM.LETT. V. 15 5187 2005 JRNL REFN ISSN 0960-894X JRNL PMID 16202589 JRNL DOI 10.1016/J.BMCL.2005.08.092 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.1.24 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 88.6 REMARK 3 NUMBER OF REFLECTIONS : 38213 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) : 0.198 REMARK 3 R VALUE (WORKING SET) : 0.195 REMARK 3 FREE R VALUE : 0.254 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2025 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.95 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1701 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.3370 REMARK 3 BIN FREE R VALUE SET COUNT : 75 REMARK 3 BIN FREE R VALUE : 0.3880 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3303 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 60 REMARK 3 SOLVENT ATOMS : 499 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.21 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.23000 REMARK 3 B22 (A**2) : -0.53000 REMARK 3 B33 (A**2) : 0.30000 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 OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.162 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.163 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.119 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.395 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.958 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.932 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3428 ; 0.018 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4629 ; 1.652 ; 1.980 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 418 ; 6.866 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 522 ; 0.114 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2534 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1675 ; 0.220 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 372 ; 0.164 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 63 ; 0.231 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 31 ; 0.168 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 2076 ; 0.958 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3353 ; 1.726 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1352 ; 2.786 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1276 ; 4.561 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS. SLIGHT DISORDER IN THE B-CHAIN BETWEEN RESIDUES 105- REMARK 3 112. REMARK 4 REMARK 4 2BZ5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 11-AUG-05. REMARK 100 THE DEPOSITION ID IS D_1290025287. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-MAR-05 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 6.50 REMARK 200 NUMBER OF CRYSTALS USED : 1 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 : OSMIC BLUE MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU IMAGE PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : D*TREK REMARK 200 DATA SCALING SOFTWARE : D*TREK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 40240 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 88.6 REMARK 200 DATA REDUNDANCY : 3.190 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 11.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.97 REMARK 200 COMPLETENESS FOR SHELL (%) : 56.0 REMARK 200 DATA REDUNDANCY IN SHELL : 2.12 REMARK 200 R MERGE FOR SHELL (I) : 0.31000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 1UY6 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.80 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: CRYSTALLIZATION CONDITIONS: 25% PEG REMARK 280 MME 2000, 0.1M NA CACODYLATE, PH6.5, 0.2M MGCL2., PH 6.50 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 32.23000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 44.28100 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 32.23000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 44.28100 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PQS REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PQS REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 400 REMARK 400 COMPOUND REMARK 400 PROTEIN HAS ATPASE ACTIVITY REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 PRO A 2 REMARK 465 GLU A 3 REMARK 465 GLU A 4 REMARK 465 THR A 5 REMARK 465 GLN A 6 REMARK 465 THR A 7 REMARK 465 GLN A 8 REMARK 465 ASP A 9 REMARK 465 GLN A 10 REMARK 465 PRO A 11 REMARK 465 MET A 12 REMARK 465 GLU A 13 REMARK 465 GLU A 14 REMARK 465 GLU A 15 REMARK 465 ARG A 226 REMARK 465 ASP A 227 REMARK 465 LYS A 228 REMARK 465 GLU A 229 REMARK 465 VAL A 230 REMARK 465 SER A 231 REMARK 465 ASP A 232 REMARK 465 ASP A 233 REMARK 465 GLU A 234 REMARK 465 ALA A 235 REMARK 465 GLU A 236 REMARK 465 PRO B 2 REMARK 465 GLU B 3 REMARK 465 GLU B 4 REMARK 465 THR B 5 REMARK 465 GLN B 6 REMARK 465 THR B 7 REMARK 465 GLN B 8 REMARK 465 ASP B 9 REMARK 465 GLN B 10 REMARK 465 PRO B 11 REMARK 465 MET B 12 REMARK 465 GLU B 13 REMARK 465 GLU B 14 REMARK 465 GLU B 15 REMARK 465 ARG B 226 REMARK 465 ASP B 227 REMARK 465 LYS B 228 REMARK 465 GLU B 229 REMARK 465 VAL B 230 REMARK 465 SER B 231 REMARK 465 ASP B 232 REMARK 465 ASP B 233 REMARK 465 GLU B 234 REMARK 465 ALA B 235 REMARK 465 GLU B 236 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 SER B 31 OG REMARK 470 GLU B 158 CG CD REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O LEU B 107 O HOH B 2124 2.04 REMARK 500 O ASP B 102 N ASN B 106 2.09 REMARK 500 O ASN B 105 CA GLY B 108 2.10 REMARK 500 O GLY B 108 O HOH B 2125 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH B 2064 O HOH B 2064 2655 2.16 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 60 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 GLY B 108 N - CA - C ANGL. DEV. = 16.8 DEGREES REMARK 500 REMARK 500 REMARK: NULL 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 TYR A 38 109.93 -160.83 REMARK 500 ALA A 111 -120.12 49.00 REMARK 500 ALA A 166 -133.73 59.33 REMARK 500 GLU A 178 76.48 -150.07 REMARK 500 ARG A 182 129.26 -175.27 REMARK 500 ASP B 66 86.32 -151.35 REMARK 500 THR B 94 41.13 -108.34 REMARK 500 ASN B 106 3.76 -57.05 REMARK 500 ILE B 110 -5.70 72.79 REMARK 500 GLN B 123 -45.71 109.68 REMARK 500 ALA B 166 -140.79 66.16 REMARK 500 LYS B 224 -6.68 -57.22 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 LEU B 107 GLY B 108 -34.21 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 AB4 A1226 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE AB4 B1226 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1BYQ RELATED DB: PDB REMARK 900 HSP90 N-TERMINAL DOMAIN BOUND TO ADP-MG REMARK 900 RELATED ID: 1OSF RELATED DB: PDB REMARK 900 HUMAN HSP90 IN COMPLEX WITH 17-DESMETHOXY- 17-N,N- REMARK 900 DIMETHYLAMINOETHYLAMINO-GELDANAMYCIN REMARK 900 RELATED ID: 1UY6 RELATED DB: PDB REMARK 900 HUMAN HSP90-ALPHA WITH 9-BUTYL-8-(3,4,5- TRIMETHOXY-BENZYL)-9H- REMARK 900 PURIN-6-YLAMINE REMARK 900 RELATED ID: 1UY7 RELATED DB: PDB REMARK 900 HUMAN HSP90-ALPHA WITH 9-BUTYL-8- (4-METHOXY-BENZYL)-9H-PURIN-6- REMARK 900 YLAMINE REMARK 900 RELATED ID: 1UY8 RELATED DB: PDB REMARK 900 HUMAN HSP90-ALPHA WITH 9-BUTYL-8- (3-TRIMETHOXY-BENZYL)-9H-PURIN- REMARK 900 6YLAMINE REMARK 900 RELATED ID: 1UY9 RELATED DB: PDB REMARK 900 HUMAN HSP90-ALPHA WITH 8-BENZO[1,3] DIOXOL-,5-YLMETHYL-9-BUTYL-9H- REMARK 900 PURIN-6- YLAMINE REMARK 900 RELATED ID: 1UYC RELATED DB: PDB REMARK 900 HUMAN HSP90-ALPHA WITH 9-BUTYL-8-(2,5- DIMETHOXY-BENZYL)-9H-PURIN-6- REMARK 900 YLAMINE REMARK 900 RELATED ID: 1UYD RELATED DB: PDB REMARK 900 HUMAN HSP90-ALPHA WITH 9-BUTYL-8- (2-CHLORO-3,4,5-TRIMETHOXY-BENZYL) REMARK 900 -9H-PURIN- 6-YLAMINE REMARK 900 RELATED ID: 1UYE RELATED DB: PDB REMARK 900 HUMAN HSP90-ALPHA WITH 8-(2-CHLORO-3,4,5- TRIMETHOXY-BENZYL)-9-PENT- REMARK 900 4-YLNYL-9H- PURIN-6-YLAMINE REMARK 900 RELATED ID: 1UYF RELATED DB: PDB REMARK 900 HUMAN HSP90-ALPHA WITH 8-(2-CHLORO-3,4, 5-TRIMETHOXY-BENZYL)-2- REMARK 900 FLUORO-9-PENT-4- YLNYL-9H-PURIN-6-YLAMINE REMARK 900 RELATED ID: 1UYG RELATED DB: PDB REMARK 900 HUMAN HSP90-ALPHA WITH 8-(2,5-DIMETHOXY- BENZYL)-2-FLUORO-9H-PURIN- REMARK 900 6-YLAMINE REMARK 900 RELATED ID: 1UYH RELATED DB: PDB REMARK 900 HUMAN HSP90-ALPHA WITH 9-BUTYL-8-(2,5- DIMETHOXY-BENZYL)-2-FLUORO- REMARK 900 9H-PURIN-6- YLAMINE REMARK 900 RELATED ID: 1UYI RELATED DB: PDB REMARK 900 HUMAN HSP90-ALPHA WITH 8-(2,5-DIMETHOXY- BENZYL)-2-FLUORO-9-PENT-9H- REMARK 900 PURIN-6- YLAMINE REMARK 900 RELATED ID: 1UYK RELATED DB: PDB REMARK 900 HUMAN HSP90-ALPHA WITH 8-BENZO[1,3] DIOXOL-,5-YLMETHYL-9-BUTYL-2- REMARK 900 FLUORO-9H- PURIN-6-YLAMINE REMARK 900 RELATED ID: 1UYL RELATED DB: PDB REMARK 900 STRUCTURE-ACTIVITY RELATIONSHIPS IN PURINE- BASED INHIBITOR BINDING REMARK 900 TO HSP90 ISOFORMS REMARK 900 RELATED ID: 1YC1 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURES OF HUMAN HSP90ALPHA COMPLEXED REMARK 900 WITHDIHYDROXYPHENYLPYRAZOLES REMARK 900 RELATED ID: 1YC3 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN HSP90ALPHA COMPLEXED REMARK 900 WITHDIHYDROXYPHENYLPYRAZOLES REMARK 900 RELATED ID: 1YC4 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN HSP90ALPHA COMPLEXED REMARK 900 WITHDIHYDROXYPHENYLPYRAZOLES REMARK 900 RELATED ID: 1YER RELATED DB: PDB REMARK 900 HUMAN HSP90 GELDANAMYCIN-BINDING DOMAIN, "CLOSED" CONFORMATION REMARK 900 RELATED ID: 1YES RELATED DB: PDB REMARK 900 HUMAN HSP90 GELDANAMYCIN-BINDING DOMAIN, "OPEN" CONFORMATION REMARK 900 RELATED ID: 1YET RELATED DB: PDB REMARK 900 GELDANAMYCIN BOUND TO THE HSP90 GELDANAMYCIN- BINDING DOMAIN REMARK 900 RELATED ID: 2BSM RELATED DB: PDB REMARK 900 NOVEL, POTENT SMALL MOLECULE INHIBITORS OF THE MOLECULAR CHAPERONE REMARK 900 HSP90 DISCOVERED THROUGH STRUCTURE-BASED DESIGN REMARK 900 RELATED ID: 2BT0 RELATED DB: PDB REMARK 900 NOVEL, POTENT SMALL MOLECULE INHIBITORS OF THE MOLECULAR CHAPERONE REMARK 900 HSP90 DISCOVERED THROUGH STRUCTURE-BASED DESIGN REMARK 900 RELATED ID: 2BYH RELATED DB: PDB REMARK 900 3-(5-CHLORO-2,4-DIHYDROXYPHENYL)-PYRAZOLE- 4-CARBOXAMIDES AS REMARK 900 INHIBITORS OF THE HSP90 MOLECULAR CHAPERONE REMARK 900 RELATED ID: 2BYI RELATED DB: PDB REMARK 900 3-(5-CHLORO-2,4-DIHYDROXYPHENYL)-PYRAZOLE- 4-CARBOXAMIDES AS REMARK 900 INHIBITORS OF THE HSP90 MOLECULAR CHAPERONE REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE CONFLICT T62S IS ALSO MENTIONED IN THE UNIPROT REFERENCES DBREF 2BZ5 A 2 236 UNP P07900 HS90A_HUMAN 1 235 DBREF 2BZ5 B 2 236 UNP P07900 HS90A_HUMAN 1 235 SEQADV 2BZ5 SER A 63 UNP P07900 THR 62 CONFLICT SEQADV 2BZ5 SER B 63 UNP P07900 THR 62 CONFLICT SEQRES 1 A 235 PRO GLU GLU THR GLN THR GLN ASP GLN PRO MET GLU GLU SEQRES 2 A 235 GLU GLU VAL GLU THR PHE ALA PHE GLN ALA GLU ILE ALA SEQRES 3 A 235 GLN LEU MET SER LEU ILE ILE ASN THR PHE TYR SER ASN SEQRES 4 A 235 LYS GLU ILE PHE LEU ARG GLU LEU ILE SER ASN SER SER SEQRES 5 A 235 ASP ALA LEU ASP LYS ILE ARG TYR GLU SER LEU THR ASP SEQRES 6 A 235 PRO SER LYS LEU ASP SER GLY LYS GLU LEU HIS ILE ASN SEQRES 7 A 235 LEU ILE PRO ASN LYS GLN ASP ARG THR LEU THR ILE VAL SEQRES 8 A 235 ASP THR GLY ILE GLY MET THR LYS ALA ASP LEU ILE ASN SEQRES 9 A 235 ASN LEU GLY THR ILE ALA LYS SER GLY THR LYS ALA PHE SEQRES 10 A 235 MET GLU ALA LEU GLN ALA GLY ALA ASP ILE SER MET ILE SEQRES 11 A 235 GLY GLN PHE GLY VAL GLY PHE TYR SER ALA TYR LEU VAL SEQRES 12 A 235 ALA GLU LYS VAL THR VAL ILE THR LYS HIS ASN ASP ASP SEQRES 13 A 235 GLU GLN TYR ALA TRP GLU SER SER ALA GLY GLY SER PHE SEQRES 14 A 235 THR VAL ARG THR ASP THR GLY GLU PRO MET GLY ARG GLY SEQRES 15 A 235 THR LYS VAL ILE LEU HIS LEU LYS GLU ASP GLN THR GLU SEQRES 16 A 235 TYR LEU GLU GLU ARG ARG ILE LYS GLU ILE VAL LYS LYS SEQRES 17 A 235 HIS SER GLN PHE ILE GLY TYR PRO ILE THR LEU PHE VAL SEQRES 18 A 235 GLU LYS GLU ARG ASP LYS GLU VAL SER ASP ASP GLU ALA SEQRES 19 A 235 GLU SEQRES 1 B 235 PRO GLU GLU THR GLN THR GLN ASP GLN PRO MET GLU GLU SEQRES 2 B 235 GLU GLU VAL GLU THR PHE ALA PHE GLN ALA GLU ILE ALA SEQRES 3 B 235 GLN LEU MET SER LEU ILE ILE ASN THR PHE TYR SER ASN SEQRES 4 B 235 LYS GLU ILE PHE LEU ARG GLU LEU ILE SER ASN SER SER SEQRES 5 B 235 ASP ALA LEU ASP LYS ILE ARG TYR GLU SER LEU THR ASP SEQRES 6 B 235 PRO SER LYS LEU ASP SER GLY LYS GLU LEU HIS ILE ASN SEQRES 7 B 235 LEU ILE PRO ASN LYS GLN ASP ARG THR LEU THR ILE VAL SEQRES 8 B 235 ASP THR GLY ILE GLY MET THR LYS ALA ASP LEU ILE ASN SEQRES 9 B 235 ASN LEU GLY THR ILE ALA LYS SER GLY THR LYS ALA PHE SEQRES 10 B 235 MET GLU ALA LEU GLN ALA GLY ALA ASP ILE SER MET ILE SEQRES 11 B 235 GLY GLN PHE GLY VAL GLY PHE TYR SER ALA TYR LEU VAL SEQRES 12 B 235 ALA GLU LYS VAL THR VAL ILE THR LYS HIS ASN ASP ASP SEQRES 13 B 235 GLU GLN TYR ALA TRP GLU SER SER ALA GLY GLY SER PHE SEQRES 14 B 235 THR VAL ARG THR ASP THR GLY GLU PRO MET GLY ARG GLY SEQRES 15 B 235 THR LYS VAL ILE LEU HIS LEU LYS GLU ASP GLN THR GLU SEQRES 16 B 235 TYR LEU GLU GLU ARG ARG ILE LYS GLU ILE VAL LYS LYS SEQRES 17 B 235 HIS SER GLN PHE ILE GLY TYR PRO ILE THR LEU PHE VAL SEQRES 18 B 235 GLU LYS GLU ARG ASP LYS GLU VAL SER ASP ASP GLU ALA SEQRES 19 B 235 GLU HET AB4 A1226 30 HET AB4 B1226 30 HETNAM AB4 2,5-DICHLORO-N-[4-HYDROXY-3-(2-HYDROXY-1-NAPHTHYL) HETNAM 2 AB4 PHENYL]BENZENESULFONAMIDE FORMUL 3 AB4 2(C22 H15 CL2 N O4 S) FORMUL 5 HOH *499(H2 O) HELIX 1 1 GLN A 23 THR A 36 1 14 HELIX 2 2 ASN A 40 GLU A 42 5 3 HELIX 3 3 ILE A 43 ASP A 66 1 24 HELIX 4 4 PRO A 67 GLY A 73 5 7 HELIX 5 5 THR A 99 THR A 109 1 11 HELIX 6 6 GLY A 114 ALA A 124 1 11 HELIX 7 7 ASP A 127 GLY A 135 5 9 HELIX 8 8 VAL A 136 LEU A 143 5 8 HELIX 9 9 GLN A 194 LEU A 198 5 5 HELIX 10 10 GLU A 199 SER A 211 1 13 HELIX 11 11 GLN B 23 THR B 36 1 14 HELIX 12 12 GLU B 42 ASP B 66 1 25 HELIX 13 13 PRO B 67 ASP B 71 5 5 HELIX 14 14 THR B 99 ASN B 106 1 8 HELIX 15 15 ILE B 110 LEU B 122 1 13 HELIX 16 16 ASP B 127 GLY B 135 5 9 HELIX 17 17 VAL B 136 LEU B 143 5 8 HELIX 18 18 GLU B 192 LEU B 198 5 7 HELIX 19 19 GLU B 199 SER B 211 1 13 SHEET 1 AA 8 VAL A 17 ALA A 21 0 SHEET 2 AA 8 SER A 169 THR A 174 -1 O PHE A 170 N PHE A 20 SHEET 3 AA 8 TYR A 160 SER A 164 -1 O ALA A 161 N ARG A 173 SHEET 4 AA 8 ALA A 145 LYS A 153 -1 O VAL A 148 N SER A 164 SHEET 5 AA 8 GLY A 183 LEU A 190 -1 O GLY A 183 N LYS A 153 SHEET 6 AA 8 THR A 88 ASP A 93 -1 O LEU A 89 N LEU A 188 SHEET 7 AA 8 ILE A 78 ASN A 83 -1 O ASN A 79 N VAL A 92 SHEET 8 AA 8 ILE A 218 LEU A 220 1 O THR A 219 N LEU A 80 SHEET 1 BA 8 GLU B 18 ALA B 21 0 SHEET 2 BA 8 SER B 169 THR B 174 -1 O PHE B 170 N PHE B 20 SHEET 3 BA 8 TYR B 160 SER B 164 -1 O ALA B 161 N ARG B 173 SHEET 4 BA 8 ALA B 145 LYS B 153 -1 O VAL B 148 N SER B 164 SHEET 5 BA 8 GLY B 183 LEU B 190 -1 O GLY B 183 N LYS B 153 SHEET 6 BA 8 THR B 88 ASP B 93 -1 O LEU B 89 N LEU B 188 SHEET 7 BA 8 ILE B 78 ASN B 83 -1 O ASN B 79 N VAL B 92 SHEET 8 BA 8 ILE B 218 LEU B 220 1 O THR B 219 N LEU B 80 LINK CG2 THR B 109 CL24 AB4 B1226 1555 1555 1.94 SITE 1 AC1 14 ASN A 51 ASP A 54 ALA A 55 LYS A 58 SITE 2 AC1 14 ASP A 93 ILE A 96 GLY A 97 MET A 98 SITE 3 AC1 14 ASN A 106 LEU A 107 PHE A 138 THR A 184 SITE 4 AC1 14 HOH A2148 HOH A2284 SITE 1 AC2 17 ASN B 51 ASP B 54 ALA B 55 LYS B 58 SITE 2 AC2 17 ASP B 93 ILE B 96 GLY B 97 MET B 98 SITE 3 AC2 17 ASN B 106 THR B 109 GLY B 135 PHE B 138 SITE 4 AC2 17 THR B 184 VAL B 186 HOH B2061 HOH B2112 SITE 5 AC2 17 HOH B2140 CRYST1 64.460 88.562 98.960 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 0.015513 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011292 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010105 0.00000