HEADER CHAPERONE 30-APR-20 7C04 TITLE CRYSTAL STRUCTURE OF HUMAN TRAP1 WITH DN203492 COMPND MOL_ID: 1; COMPND 2 MOLECULE: HEAT SHOCK PROTEIN 75 KDA, MITOCHONDRIAL; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: HSP 75,TNFR-ASSOCIATED PROTEIN 1,TUMOR NECROSIS FACTOR TYPE COMPND 5 1 RECEPTOR-ASSOCIATED PROTEIN,TRAP-1; 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 GENE: TRAP1, HSP75; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) KEYWDS TRAP1, SELECTIVITY, MITOCHONDRIA, HSP90, ANTICANCER, DRUG, CHAPERONE EXPDTA X-RAY DIFFRACTION AUTHOR D.KIM,D.KIM,S.Y.KIM,J.H.LEE,B.H.KANG,S.KANG,C.LEE REVDAT 2 29-NOV-23 7C04 1 REMARK REVDAT 1 08-JUL-20 7C04 0 JRNL AUTH D.KIM,S.Y.KIM,D.KIM,N.G.YOON,J.YUN,K.B.HONG,C.LEE,J.H.LEE, JRNL AUTH 2 B.H.KANG,S.KANG JRNL TITL DEVELOPMENT OF PYRAZOLO[3,4-D]PYRIMIDINE-6-AMINE-BASED TRAP1 JRNL TITL 2 INHIBITORS THAT DEMONSTRATE IN VIVO ANTICANCER ACTIVITY IN JRNL TITL 3 MOUSE XENOGRAFT MODELS. JRNL REF BIOORG.CHEM. V. 101 03901 2020 JRNL REFN ISSN 0045-2068 JRNL PMID 32590225 JRNL DOI 10.1016/J.BIOORG.2020.103901 REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.9_1692 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.21 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 2.060 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 29611 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.191 REMARK 3 R VALUE (WORKING SET) : 0.189 REMARK 3 FREE R VALUE : 0.234 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.002 REMARK 3 FREE R VALUE TEST SET COUNT : 1481 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 24.2100 - 3.7715 0.98 2522 132 0.1599 0.2036 REMARK 3 2 3.7715 - 2.9953 1.00 2567 135 0.1845 0.2420 REMARK 3 3 2.9953 - 2.6172 1.00 2583 136 0.2005 0.2334 REMARK 3 4 2.6172 - 2.3781 1.00 2575 136 0.2020 0.2332 REMARK 3 5 2.3781 - 2.2078 1.00 2548 131 0.1982 0.2619 REMARK 3 6 2.2078 - 2.0777 1.00 2561 138 0.1940 0.2229 REMARK 3 7 2.0777 - 1.9737 1.00 2574 137 0.1993 0.2420 REMARK 3 8 1.9737 - 1.8878 1.00 2583 131 0.2082 0.2452 REMARK 3 9 1.8878 - 1.8152 0.99 2557 134 0.2368 0.2841 REMARK 3 10 1.8152 - 1.7526 0.99 2535 135 0.2423 0.2968 REMARK 3 11 1.7526 - 1.7000 0.98 2525 136 0.2709 0.2862 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.195 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.634 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 26.83 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 36.33 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 : 0.005 1769 REMARK 3 ANGLE : 0.847 2385 REMARK 3 CHIRALITY : 0.033 268 REMARK 3 PLANARITY : 0.003 304 REMARK 3 DIHEDRAL : 13.148 645 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 7C04 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 03-MAY-20. REMARK 100 THE DEPOSITION ID IS D_1300016795. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-JUL-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PAL/PLS REMARK 200 BEAMLINE : 7A (6B, 6C1) REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 270 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 29618 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 (%) : 99.4 REMARK 200 DATA REDUNDANCY : 3.200 REMARK 200 R MERGE (I) : 0.04500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 32.1000 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) : 1.73 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.36300 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: NULL REMARK 200 STARTING MODEL: 5Y3N REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.58 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.71 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M CITRATE PH 5.5, 31% PEG 4000, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 X+2/3,Y+1/3,Z+1/3 REMARK 290 5555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 6555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 7555 X+1/3,Y+2/3,Z+2/3 REMARK 290 8555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 9555 -X+Y+1/3,-X+2/3,Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 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 55.20250 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 31.87118 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 19.81500 REMARK 290 SMTRY1 5 -0.500000 -0.866025 0.000000 55.20250 REMARK 290 SMTRY2 5 0.866025 -0.500000 0.000000 31.87118 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 19.81500 REMARK 290 SMTRY1 6 -0.500000 0.866025 0.000000 55.20250 REMARK 290 SMTRY2 6 -0.866025 -0.500000 0.000000 31.87118 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 19.81500 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 63.74236 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 39.63000 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 63.74236 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 39.63000 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 63.74236 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 39.63000 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 SER A 60 REMARK 465 THR A 61 REMARK 465 GLN A 62 REMARK 465 THR A 63 REMARK 465 ALA A 64 REMARK 465 GLU A 65 REMARK 465 ASP A 66 REMARK 465 LYS A 67 REMARK 465 GLU A 68 REMARK 465 GLU A 69 REMARK 465 PRO A 70 REMARK 465 THR A 294 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 GLN A 82 34.90 -140.80 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 FEU A 301 DBREF 7C04 A 60 294 UNP Q12931 TRAP1_HUMAN 60 294 SEQRES 1 A 235 SER THR GLN THR ALA GLU ASP LYS GLU GLU PRO LEU HIS SEQRES 2 A 235 SER ILE ILE SER SER THR GLU SER VAL GLN GLY SER THR SEQRES 3 A 235 SER LYS HIS GLU PHE GLN ALA GLU THR LYS LYS LEU LEU SEQRES 4 A 235 ASP ILE VAL ALA ARG SER LEU TYR SER GLU LYS GLU VAL SEQRES 5 A 235 PHE ILE ARG GLU LEU ILE SER ASN ALA SER ASP ALA LEU SEQRES 6 A 235 GLU LYS LEU ARG HIS LYS LEU VAL SER ASP GLY GLN ALA SEQRES 7 A 235 LEU PRO GLU MET GLU ILE HIS LEU GLN THR ASN ALA GLU SEQRES 8 A 235 LYS GLY THR ILE THR ILE GLN ASP THR GLY ILE GLY MET SEQRES 9 A 235 THR GLN GLU GLU LEU VAL SER ASN LEU GLY THR ILE ALA SEQRES 10 A 235 ARG SER GLY SER LYS ALA PHE LEU ASP ALA LEU GLN ASN SEQRES 11 A 235 GLN ALA GLU ALA SER SER LYS ILE ILE GLY GLN PHE GLY SEQRES 12 A 235 VAL GLY PHE TYR SER ALA PHE MET VAL ALA ASP ARG VAL SEQRES 13 A 235 GLU VAL TYR SER ARG SER ALA ALA PRO GLY SER LEU GLY SEQRES 14 A 235 TYR GLN TRP LEU SER ASP GLY SER GLY VAL PHE GLU ILE SEQRES 15 A 235 ALA GLU ALA SER GLY VAL ARG THR GLY THR LYS ILE ILE SEQRES 16 A 235 ILE HIS LEU LYS SER ASP CYS LYS GLU PHE SER SER GLU SEQRES 17 A 235 ALA ARG VAL ARG ASP VAL VAL THR LYS TYR SER ASN PHE SEQRES 18 A 235 VAL SER PHE PRO LEU TYR LEU ASN GLY ARG ARG MET ASN SEQRES 19 A 235 THR HET FEU A 301 35 HETNAM FEU 4-CHLORANYL-1-[[2-METHOXY-4-(TRIFLUOROMETHYL) HETNAM 2 FEU PHENYL]METHYL]PYRAZOLO[3,4-D]PYRIMIDIN-6-AMINE FORMUL 2 FEU C14 H11 CL F3 N5 O FORMUL 3 HOH *130(H2 O) HELIX 1 AA1 GLU A 93 TYR A 106 1 14 HELIX 2 AA2 SER A 107 LYS A 109 5 3 HELIX 3 AA3 GLU A 110 GLY A 135 1 26 HELIX 4 AA4 THR A 164 ASN A 171 1 8 HELIX 5 AA5 GLY A 173 GLY A 179 1 7 HELIX 6 AA6 SER A 180 GLN A 190 1 11 HELIX 7 AA7 ALA A 193 PHE A 201 1 9 HELIX 8 AA8 PHE A 205 VAL A 211 1 7 HELIX 9 AA9 CYS A 261 SER A 265 5 5 HELIX 10 AB1 SER A 266 THR A 275 1 10 HELIX 11 AB2 LYS A 276 VAL A 281 5 6 SHEET 1 AA1 3 SER A 80 VAL A 81 0 SHEET 2 AA1 3 VAL A 238 SER A 245 -1 O SER A 245 N SER A 80 SHEET 3 AA1 3 SER A 86 GLU A 89 -1 N SER A 86 O ILE A 241 SHEET 1 AA2 9 SER A 80 VAL A 81 0 SHEET 2 AA2 9 VAL A 238 SER A 245 -1 O SER A 245 N SER A 80 SHEET 3 AA2 9 TYR A 229 SER A 233 -1 N GLN A 230 O ALA A 242 SHEET 4 AA2 9 ALA A 212 ARG A 220 -1 N VAL A 215 O SER A 233 SHEET 5 AA2 9 GLY A 250 LEU A 257 -1 O ILE A 254 N GLU A 216 SHEET 6 AA2 9 THR A 153 ASP A 158 -1 N ILE A 154 O ILE A 255 SHEET 7 AA2 9 ILE A 143 ASN A 148 -1 N HIS A 144 O GLN A 157 SHEET 8 AA2 9 LEU A 285 LEU A 287 1 O TYR A 286 N ILE A 143 SHEET 9 AA2 9 ARG A 290 ARG A 291 -1 O ARG A 290 N LEU A 287 SITE 1 AC1 14 ALA A 123 ASP A 158 ILE A 161 GLY A 162 SITE 2 AC1 14 MET A 163 GLU A 167 LEU A 168 LEU A 172 SITE 3 AC1 14 PHE A 205 TRP A 231 THR A 251 HOH A 449 SITE 4 AC1 14 HOH A 504 HOH A 516 CRYST1 110.405 110.405 59.445 90.00 90.00 120.00 H 3 9 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 0.009058 0.005229 0.000000 0.00000 SCALE2 0.000000 0.010459 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016822 0.00000