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- PDB-5y3n: Structure of TRAP1 complexed with DN401 -

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Basic information

Entry
Database: PDB / ID: 5y3n
TitleStructure of TRAP1 complexed with DN401
ComponentsHeat shock protein 75 kDa, mitochondrialHeat shock response
KeywordsCHAPERONE / TRAP1 / Inhibitor / DN401 / Mitochondrial HSP90
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-8MF / Heat shock protein 75 kDa, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.4 Å
AuthorsJeong, H. / Park, H.K. / Kang, S. / Kang, B.H. / Lee, C.
CitationJournal: J. Med. Chem. / Year: 2017
Title: Paralog Specificity Determines Subcellular Distribution, Action Mechanism, and Anticancer Activity of TRAP1 Inhibitors.
Authors: Park, H.K. / Jeong, H. / Ko, E. / Lee, G. / Lee, J.E. / Lee, S.K. / Lee, A.J. / Im, J.Y. / Hu, S. / Kim, S.H. / Lee, J.H. / Lee, C. / Kang, S. / Kang, B.H.
History
DepositionJul 29, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 30, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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)57,8052
Polymers57,4221
Non-polymers3831
Water1,04558
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 area22320 Å2
Unit cell
Length a, b, c (Å)69.410, 69.410, 252.159
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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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: 57422.090 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 60-561
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRAP1, HSP75 / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: Q12931
#2: Chemical ChemComp-8MF / 1-[(6-bromanyl-1,3-benzodioxol-5-yl)methyl]-4-chloranyl-pyrazolo[3,4-d]pyrimidin-6-amine


Mass: 382.600 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H9BrClN5O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 58 / Source method: isolated from a natural source / Formula: H2O

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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: 2.64 Å3/Da / Density % sol: 53.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG 8000, sodium cacodylate, calcium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9796 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 24, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 25006 / % possible obs: 99.1 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.03 / Net I/σ(I): 40
Reflection shellResolution: 2.4→2.44 Å

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
Cootmodel building
RefinementResolution: 2.4→34.705 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2573 1250 5 %
Rwork0.208 --
obs0.2105 24985 99.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→34.705 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3550 0 22 58 3630
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043641
X-RAY DIFFRACTIONf_angle_d0.7824908
X-RAY DIFFRACTIONf_dihedral_angle_d13.9261367
X-RAY DIFFRACTIONf_chiral_restr0.029539
X-RAY DIFFRACTIONf_plane_restr0.003620
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4001-2.49620.31541360.24772566X-RAY DIFFRACTION100
2.4962-2.60970.30341340.23532561X-RAY DIFFRACTION100
2.6097-2.74730.32071370.23752611X-RAY DIFFRACTION100
2.7473-2.91930.27121380.23212607X-RAY DIFFRACTION100
2.9193-3.14460.25751370.23492623X-RAY DIFFRACTION100
3.1446-3.46080.26931390.21492621X-RAY DIFFRACTION100
3.4608-3.96090.22281390.19362645X-RAY DIFFRACTION100
3.9609-4.9880.22831420.18272704X-RAY DIFFRACTION99
4.988-34.70860.27181480.21052797X-RAY DIFFRACTION97
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.85861.32191.59613.04951.39233.472-0.25110.8857-0.2084-0.55210.35431.06040.29260.0696-0.01441.0729-0.0708-0.45040.491-0.03830.782115.89750.006921.9363
22.8302-1.325-0.21475.25960.59443.00380.07710.3777-0.0002-0.61530.06570.48480.0562-0.099-0.06651.009-0.0222-0.43340.40980.02030.583212.497810.582220.2426
33.9451-2.10981.41922.7071-1.8794.1187-0.0270.0346-0.0680.14670.34910.18520.4553-0.1517-0.35920.8118-0.0403-0.44320.51890.26860.6636-2.795636.660218.7501
44.28651.07250.43093.09060.24715.1390.2289-0.47440.07850.50480.24830.7455-0.5071-1.342-0.44310.72730.0964-0.11910.89450.47120.9776-21.391558.000811.4892
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 70 through 93 )
2X-RAY DIFFRACTION2chain 'A' and (resid 94 through 297 )
3X-RAY DIFFRACTION3chain 'A' and (resid 298 through 434 )
4X-RAY DIFFRACTION4chain 'A' and (resid 435 through 552 )

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