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- PDB-7c7c: Crystal structure of human TRAP1 with SJT104 -

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Basic information

Entry
Database: PDB / ID: 7c7c
TitleCrystal structure of human TRAP1 with SJT104
ComponentsHeat shock protein 75 kDa, mitochondrialHeat shock response
KeywordsCHAPERONE / TRPA1 / 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-FK0 / Heat shock protein 75 kDa, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 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)57,7952
Polymers57,4221
Non-polymers3731
Water0
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 area22170 Å2
Unit cell
Length a, b, c (Å)69.543, 69.543, 251.327
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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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
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-FK0 / 2-azanyl-9-[(4-bromanyl-2-fluoranyl-phenyl)methyl]-6-chloranyl-purin-8-ol


Mass: 372.580 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H8BrClFN5O / Feature type: SUBJECT OF INVESTIGATION
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: 2.65 Å3/Da / Density % sol: 53.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.76
Details: 0.1M Cacodylate pH 6.76, 0.1M Calcium acetate, 18% PEG 5000 MME

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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: Mar 22, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 13023 / % possible obs: 98.8 % / Redundancy: 9.9 % / Biso Wilson estimate: 74.75 Å2 / Rmerge(I) obs: 0.107 / Net I/σ(I): 17.7
Reflection shellResolution: 3→3.05 Å / Rmerge(I) obs: 0.52 / Num. unique obs: 13023

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Processing

Software
NameVersionClassification
HKL-2000data processing
PHENIX1.14_3260refinement
Cootmodel building
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5Y3N

5y3n


Resolution: 3→24.98 Å / SU ML: 0.4771 / Cross valid method: FREE R-VALUE / σ(F): 1.44 / Phase error: 28.9653 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.303 649 5 %
Rwork0.2321 12322 -
obs0.2356 12971 99.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 90.32 Å2
Refinement stepCycle: LAST / Resolution: 3→24.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3479 0 21 0 3500
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00153570
X-RAY DIFFRACTIONf_angle_d0.40254812
X-RAY DIFFRACTIONf_chiral_restr0.0352530
X-RAY DIFFRACTIONf_plane_restr0.0024607
X-RAY DIFFRACTIONf_dihedral_angle_d5.84122156
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.230.38611230.29722347X-RAY DIFFRACTION97.78
3.23-3.560.35881280.26852418X-RAY DIFFRACTION99.26
3.56-4.070.31280.22532441X-RAY DIFFRACTION99.15
4.07-5.120.2851300.21482468X-RAY DIFFRACTION99.16
5.12-24.980.2791400.21982648X-RAY DIFFRACTION99.68
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)
12.99260591957-0.1066296713140.4345592994223.962958466490.08838704714992.854840565420.008142100758620.2466818958590.0486969160294-0.1628227783460.08496221366020.482815793765-0.00876868778009-0.0251866030973-0.05563118277750.975623094074-0.00826157118903-0.4886707735050.4088880978010.05103391582670.66411550835612.79052737058.6168893372220.1788589855
23.10787399352-3.636024115991.331995698934.46097645928-1.988211616943.38582031309-0.0476836419351-0.305413682304-0.2236945708940.4085586954480.4164215560750.7360194179180.0289654117101-0.565094687646-0.2967372751350.722240222353-0.0463264553934-0.3485292930120.6717726677790.2999456541690.839689237018-10.903562165946.249050452815.3957618305
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 70 through 292 )
2X-RAY DIFFRACTION2chain 'A' and (resid 293 through 552 )

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