HEADER CHAPERONE/INHIBITOR 15-SEP-20 7D25 TITLE HSP90 ALPHA N-TERMINAL DOMAIN IN COMPLEX WITH A 14 COMPUND COMPND MOL_ID: 1; COMPND 2 MOLECULE: HEAT SHOCK PROTEIN HSP 90-ALPHA; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: HEAT SHOCK 86 KDA,HSP86,TUMOR-SPECIFIC TRANSPLANTATION 86 COMPND 5 KDA ANTIGEN,TSTA; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: HSP90AA1, HSP86, HSP86-1, HSPCA; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS CHAPERONE-INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR S.C.SHIN,E.E.KIM REVDAT 2 29-NOV-23 7D25 1 REMARK REVDAT 1 28-JUL-21 7D25 0 JRNL AUTH S.C.SHIN,A.K.EL-DAMASY,J.H.LEE,S.H.SEO,J.H.KIM,Y.H.SEO, JRNL AUTH 2 Y.LEE,J.H.YU,E.K.BANG,E.E.KIM,G.KEUM JRNL TITL STRUCTURAL BASIS FOR DESIGN OF NEW PURINE-BASED INHIBITORS JRNL TITL 2 TARGETING THE HYDROPHOBIC BINDING POCKET OF HSP90. JRNL REF INT J MOL SCI V. 21 2020 JRNL REFN ESSN 1422-0067 JRNL PMID 33317068 JRNL DOI 10.3390/IJMS21249377 REMARK 2 REMARK 2 RESOLUTION. 1.65 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.16_3549 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.65 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.96 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.500 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 3 NUMBER OF REFLECTIONS : 35747 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.188 REMARK 3 R VALUE (WORKING SET) : 0.186 REMARK 3 FREE R VALUE : 0.214 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.590 REMARK 3 FREE R VALUE TEST SET COUNT : 2000 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 34.9610 - 3.9747 0.99 2567 153 0.1748 0.1917 REMARK 3 2 3.9747 - 3.1555 1.00 2494 147 0.1750 0.1989 REMARK 3 3 3.1555 - 2.7568 1.00 2450 145 0.1941 0.2361 REMARK 3 4 2.7568 - 2.5048 0.99 2436 145 0.1866 0.1866 REMARK 3 5 2.5048 - 2.3253 0.99 2437 144 0.1841 0.2415 REMARK 3 6 2.3253 - 2.1883 0.99 2414 143 0.1750 0.1909 REMARK 3 7 2.1883 - 2.0787 0.99 2401 143 0.1740 0.2007 REMARK 3 8 2.0787 - 1.9882 0.99 2419 142 0.1794 0.2186 REMARK 3 9 1.9882 - 1.9117 0.99 2389 142 0.1889 0.2292 REMARK 3 10 1.9117 - 1.8457 0.98 2395 143 0.1976 0.2291 REMARK 3 11 1.8457 - 1.7880 0.98 2379 141 0.2046 0.2676 REMARK 3 12 1.7880 - 1.7369 0.98 2347 139 0.2233 0.2571 REMARK 3 13 1.7369 - 1.6912 0.97 2347 139 0.2250 0.2719 REMARK 3 14 1.6912 - 1.6500 0.94 2272 134 0.2438 0.2868 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.180 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.290 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.88 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 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 7D25 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 16-SEP-20. REMARK 100 THE DEPOSITION ID IS D_1300018628. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-FEB-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PAL/PLS REMARK 200 BEAMLINE : 5C (4A) REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 35747 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.650 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 (%) : 98.5 REMARK 200 DATA REDUNDANCY : 5.800 REMARK 200 R MERGE (I) : 0.05300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.65 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.71 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.5 REMARK 200 DATA REDUNDANCY IN SHELL : 3.90 REMARK 200 R MERGE FOR SHELL (I) : 0.25200 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: 5H22 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 61.46 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.19 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.0M AMMONIUM SULFATE, 0.1M TRIS-HCL REMARK 280 (PH8.5), VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 2 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,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-Z+1/2 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 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 33.80200 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 44.91400 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 49.11550 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 33.80200 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 44.91400 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 49.11550 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 33.80200 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 44.91400 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 49.11550 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 33.80200 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 44.91400 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 49.11550 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: MONOMERIC 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 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 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 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 ASN A 105 -47.55 -131.56 REMARK 500 ALA A 166 -144.02 61.97 REMARK 500 ARG A 182 137.08 -171.00 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 GQ6 A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GQ6 A 302 DBREF 7D25 A 16 224 UNP P07901 HS90A_MOUSE 16 224 SEQADV 7D25 GLN A 10 UNP P07901 EXPRESSION TAG SEQADV 7D25 PRO A 11 UNP P07901 EXPRESSION TAG SEQADV 7D25 MET A 12 UNP P07901 EXPRESSION TAG SEQADV 7D25 GLU A 13 UNP P07901 EXPRESSION TAG SEQADV 7D25 GLU A 14 UNP P07901 EXPRESSION TAG SEQADV 7D25 GLU A 15 UNP P07901 EXPRESSION TAG SEQRES 1 A 215 GLN PRO MET GLU GLU GLU GLU VAL GLU THR PHE ALA PHE SEQRES 2 A 215 GLN ALA GLU ILE ALA GLN LEU MET SER LEU ILE ILE ASN SEQRES 3 A 215 THR PHE TYR SER ASN LYS GLU ILE PHE LEU ARG GLU LEU SEQRES 4 A 215 ILE SER ASN SER SER ASP ALA LEU ASP LYS ILE ARG TYR SEQRES 5 A 215 GLU SER LEU THR ASP PRO SER LYS LEU ASP SER GLY LYS SEQRES 6 A 215 GLU LEU HIS ILE ASN LEU ILE PRO SER LYS GLN ASP ARG SEQRES 7 A 215 THR LEU THR ILE VAL ASP THR GLY ILE GLY MET THR LYS SEQRES 8 A 215 ALA ASP LEU ILE ASN ASN LEU GLY THR ILE ALA LYS SER SEQRES 9 A 215 GLY THR LYS ALA PHE MET GLU ALA LEU GLN ALA GLY ALA SEQRES 10 A 215 ASP ILE SER MET ILE GLY GLN PHE GLY VAL GLY PHE TYR SEQRES 11 A 215 SER ALA TYR LEU VAL ALA GLU LYS VAL THR VAL ILE THR SEQRES 12 A 215 LYS HIS ASN ASP ASP GLU GLN TYR ALA TRP GLU SER SER SEQRES 13 A 215 ALA GLY GLY SER PHE THR VAL ARG THR ASP THR GLY GLU SEQRES 14 A 215 PRO MET GLY ARG GLY THR LYS VAL ILE LEU HIS LEU LYS SEQRES 15 A 215 GLU ASP GLN THR GLU TYR LEU GLU GLU ARG ARG ILE LYS SEQRES 16 A 215 GLU ILE VAL LYS LYS HIS SER GLN PHE ILE GLY TYR PRO SEQRES 17 A 215 ILE THR LEU PHE VAL GLU LYS HET GQ6 A 301 19 HET GQ6 A 302 19 HETNAM GQ6 6-CHLORANYL-9-[(4-METHYLPHENYL)METHYL]PURIN-2-AMINE FORMUL 2 GQ6 2(C13 H12 CL N5) FORMUL 4 HOH *310(H2 O) HELIX 1 AA1 GLN A 23 THR A 36 1 14 HELIX 2 AA2 GLU A 42 LEU A 64 1 23 HELIX 3 AA3 THR A 65 ASP A 71 5 7 HELIX 4 AA4 THR A 99 ASN A 105 1 7 HELIX 5 AA5 ASN A 105 ALA A 124 1 20 HELIX 6 AA6 ASP A 127 GLY A 135 5 9 HELIX 7 AA7 VAL A 136 LEU A 143 5 8 HELIX 8 AA8 GLU A 192 LEU A 198 5 7 HELIX 9 AA9 GLU A 199 SER A 211 1 13 SHEET 1 AA1 8 VAL A 17 ALA A 21 0 SHEET 2 AA1 8 SER A 169 THR A 174 -1 O PHE A 170 N PHE A 20 SHEET 3 AA1 8 GLN A 159 SER A 164 -1 N ALA A 161 O ARG A 173 SHEET 4 AA1 8 ALA A 145 LYS A 153 -1 N VAL A 150 O TRP A 162 SHEET 5 AA1 8 GLY A 183 LEU A 190 -1 O ILE A 187 N THR A 149 SHEET 6 AA1 8 THR A 88 ASP A 93 -1 N LEU A 89 O LEU A 188 SHEET 7 AA1 8 ILE A 78 SER A 83 -1 N ASN A 79 O VAL A 92 SHEET 8 AA1 8 ILE A 218 LEU A 220 1 O THR A 219 N LEU A 80 SITE 1 AC1 14 ASN A 51 ALA A 55 ASP A 93 ILE A 96 SITE 2 AC1 14 GLY A 97 MET A 98 PHE A 138 TRP A 162 SITE 3 AC1 14 THR A 184 GQ6 A 302 HOH A 446 HOH A 557 SITE 4 AC1 14 HOH A 561 HOH A 585 SITE 1 AC2 9 ASN A 51 LEU A 107 ALA A 111 GLY A 135 SITE 2 AC2 9 VAL A 136 GLY A 137 PHE A 138 TYR A 139 SITE 3 AC2 9 GQ6 A 301 CRYST1 67.604 89.828 98.231 90.00 90.00 90.00 I 2 2 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 0.014792 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011132 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010180 0.00000