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- PDB-7c7b: Crystal structure of human TRAP1 with SJT009 -

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Basic information

Entry
Database: PDB / ID: 7c7b
TitleCrystal structure of human TRAP1 with SJT009
ComponentsHeat shock protein 75 kDa, mitochondrialHeat shock response
KeywordsCHAPERONE / TRAP1 / selectivity / mitochondria / Hsp90 / anticancer / drug
Function / homology
Function and homology information


translational attenuation / negative regulation of cellular respiration / Respiratory electron transport / tumor necrosis factor receptor binding / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / chaperone-mediated protein folding / negative regulation of reactive oxygen species biosynthetic process / cell periphery / ATP-dependent protein folding chaperone / mitochondrial intermembrane space ...translational attenuation / negative regulation of cellular respiration / Respiratory electron transport / tumor necrosis factor receptor binding / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / chaperone-mediated protein folding / negative regulation of reactive oxygen species biosynthetic process / cell periphery / ATP-dependent protein folding chaperone / mitochondrial intermembrane space / unfolded protein binding / protein folding / mitochondrial inner membrane / mitochondrial matrix / protein kinase binding / ATP hydrolysis activity / mitochondrion / RNA binding / nucleoplasm / ATP binding / membrane
Similarity search - Function
HSP90, C-terminal domain / Heat shock protein Hsp90, N-terminal / Heat shock protein Hsp90 family / Hsp90 protein / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / Ribosomal protein S5 domain 2-type fold
Similarity search - Domain/homology
Chem-FJX / Heat shock protein 75 kDa, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsKim, D. / Yang, S. / Yoon, N.G. / Park, E. / Kim, S.Y. / Kang, B.H. / Lee, C. / Kang, S.
CitationJournal: Acs Med.Chem.Lett. / Year: 2021
Title: Design and Synthesis of TRAP1 Selective Inhibitors: H-Bonding with Asn171 Residue in TRAP1 Increases Paralog Selectivity.
Authors: Yang, S. / Yoon, N.G. / Kim, D. / Park, E. / Kim, S.Y. / Lee, J.H. / Lee, C. / Kang, B.H. / Kang, S.
History
DepositionMay 24, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 26, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 25, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Heat shock protein 75 kDa, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1782
Polymers25,7801
Non-polymers3991
Water4,378243
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10680 Å2
Unit cell
Length a, b, c (Å)109.597, 109.597, 59.895
Angle α, β, γ (deg.)90.0, 90.0, 120.0
Int Tables number146
Space group name H-MH3
Space group name HallR3
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x+1/3,y+2/3,z+2/3
#5: -y+1/3,x-y+2/3,z+2/3
#6: -x+y+1/3,-x+2/3,z+2/3
#7: x+2/3,y+1/3,z+1/3
#8: -y+2/3,x-y+1/3,z+1/3
#9: -x+y+2/3,-x+1/3,z+1/3

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Components

#1: Protein Heat shock protein 75 kDa, mitochondrial / Heat shock response / HSP 75 / TNFR-associated protein 1 / Tumor necrosis factor type 1 receptor-associated protein / TRAP-1


Mass: 25779.865 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRAP1, HSP75 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q12931
#2: Chemical ChemComp-FJX / 2-azanyl-9-[(6-bromanyl-1,3-benzodioxol-5-yl)methyl]-6-chloranyl-purin-8-ol


Mass: 398.599 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H9BrClN5O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 243 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.69 Å3/Da / Density % sol: 54.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.1M Na-acetate pH 4.6, 0.1M Ammonium acetate, 33% PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 8, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 42470 / % possible obs: 99.2 % / Redundancy: 3.1 % / Biso Wilson estimate: 17.1434013931 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 32.7
Reflection shellResolution: 1.5→1.53 Å / Rmerge(I) obs: 0.369 / Num. unique obs: 42470

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Processing

Software
NameVersionClassification
HKL-2000data processing
PHENIX1.9_1692refinement
Cootmodel building
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5Y3N

5y3n


Resolution: 1.5→24.0994377539 Å / SU ML: 0.148267550542 / Cross valid method: FREE R-VALUE / σ(F): 1.97514707622 / Phase error: 23.2077286218
RfactorNum. reflection% reflection
Rfree0.205890288013 2011 4.7355531484 %
Rwork0.173492983264 40455 -
obs0.175029741535 42466 98.9906524628 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.7195642734 Å2
Refinement stepCycle: LAST / Resolution: 1.5→24.0994377539 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1718 0 23 243 1984
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007783757385141769
X-RAY DIFFRACTIONf_angle_d1.084388845942385
X-RAY DIFFRACTIONf_chiral_restr0.0418722335428268
X-RAY DIFFRACTIONf_plane_restr0.00464801298034304
X-RAY DIFFRACTIONf_dihedral_angle_d13.2908067498646
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.50071-1.53820.2795648310811350.2522205382982759X-RAY DIFFRACTION94.8852459016
1.5382-1.57980.2413341995341420.2458298949292925X-RAY DIFFRACTION98.9993544222
1.5798-1.62630.2590481548731460.2159653416552899X-RAY DIFFRACTION99.7053045187
1.6263-1.67880.2417254492531450.2068872587542878X-RAY DIFFRACTION99.8348745046
1.6788-1.73880.2038364542261440.1911261132072956X-RAY DIFFRACTION99.8389694042
1.7388-1.80840.192253325781450.1803915214362888X-RAY DIFFRACTION99.8354180382
1.8084-1.89060.2123518745741440.1762718568452927X-RAY DIFFRACTION99.9024072869
1.8906-1.99030.212496649521430.1757084845912903X-RAY DIFFRACTION99.738048461
1.9903-2.11490.185105862371430.176849146012902X-RAY DIFFRACTION99.7706422018
2.1149-2.27810.211474249731470.1747571298572922X-RAY DIFFRACTION99.513618677
2.2781-2.50710.2106739503971440.1769523705652909X-RAY DIFFRACTION99.5759947815
2.5071-2.86940.1976969777241440.1798035505892892X-RAY DIFFRACTION98.9569752282
2.8694-3.61310.2122666679381440.1636378275112871X-RAY DIFFRACTION98.6261040236
3.6131-24.0090.1868887293871450.1483613666612824X-RAY DIFFRACTION96.6786063172

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