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- PDB-7c04: Crystal structure of human Trap1 with DN203492 -

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Basic information

Entry
Database: PDB / ID: 7c04
TitleCrystal structure of human Trap1 with DN203492
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-like ATPase, C-terminal domain / Heat Shock Protein 90 / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase ...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-like ATPase, C-terminal domain / Heat Shock Protein 90 / 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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-FEU / Heat shock protein 75 kDa, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsKim, D. / Kim, D. / Kim, S.Y. / Lee, J.H. / Kang, B.H. / Kang, S. / Lee, C.
CitationJournal: Bioorg.Chem. / Year: 2020
Title: Development of pyrazolo[3,4-d]pyrimidine-6-amine-based TRAP1 inhibitors that demonstrate in vivo anticancer activity in mouse xenograft models.
Authors: Kim, D. / Kim, S.Y. / Kim, D. / Yoon, N.G. / Yun, J. / Hong, K.B. / Lee, C. / Lee, J.H. / Kang, B.H. / Kang, S.
History
DepositionApr 30, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 8, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)26,1382
Polymers25,7801
Non-polymers3581
Water2,342130
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 area10770 Å2
Unit cell
Length a, b, c (Å)110.405, 110.405, 59.445
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-FEU / 4-chloranyl-1-[[2-methoxy-4-(trifluoromethyl)phenyl]methyl]pyrazolo[3,4-d]pyrimidin-6-amine


Mass: 357.718 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H11ClF3N5O / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 130 / 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: 2.71 Å3/Da / Density % sol: 54.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 0.1M Citrate pH 5.5, 31% PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jul 19, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 29618 / % possible obs: 99.4 % / Redundancy: 3.2 % / Biso Wilson estimate: 26.8295819249 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 32.1
Reflection shellResolution: 1.7→1.73 Å / Rmerge(I) obs: 0.363 / Num. unique obs: 29618

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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: 1.7→24.21 Å / SU ML: 0.195400541213 / Cross valid method: FREE R-VALUE / σ(F): 2.06 / Phase error: 24.6338170423
RfactorNum. reflection% reflection
Rfree0.2336 1481 5.00151970551 %
Rwork0.1893 --
obs0.1914 29611 99.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 36.3250801994 Å2
Refinement stepCycle: LAST / Resolution: 1.7→24.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1718 0 24 130 1872
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004997032778941769
X-RAY DIFFRACTIONf_angle_d0.8472773748862385
X-RAY DIFFRACTIONf_chiral_restr0.0330327869593268
X-RAY DIFFRACTIONf_plane_restr0.00316434104982304
X-RAY DIFFRACTIONf_dihedral_angle_d13.1480971144645
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.75260.2862192633361360.2708668847112525X-RAY DIFFRACTION97.7590007348
1.7526-1.81520.2968478616011350.2422917668092535X-RAY DIFFRACTION99.1091314031
1.8152-1.88780.284090051811340.2368455591052557X-RAY DIFFRACTION99.4089397857
1.8878-1.97370.2451526475181310.2082205340662583X-RAY DIFFRACTION99.6328928047
1.9737-2.07770.2420187278051370.1992520771232574X-RAY DIFFRACTION99.7424576895
2.0777-2.20780.2229167999451380.1939622823142561X-RAY DIFFRACTION99.6676514032
2.2078-2.37810.2619330865851310.1981740006322548X-RAY DIFFRACTION99.8509131569
2.3781-2.61720.2332353074821360.2019647318242575X-RAY DIFFRACTION99.7057741817
2.6172-2.99530.2333587449051360.200496362632583X-RAY DIFFRACTION99.8897869214
2.9953-3.77150.2420093203331350.1844530847422567X-RAY DIFFRACTION99.926035503
3.7715-24.210.2035591796981320.1598926905582522X-RAY DIFFRACTION97.7892409727

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