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- PDB-7u8w: hTRAP1 with inhibitors -

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Basic information

Entry
Database: PDB / ID: 7u8w
TitlehTRAP1 with inhibitors
ComponentsHeat shock protein 75 kDa, mitochondrialHeat shock response
KeywordsCHAPERONE / hTRAP1 / inhibitor
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 ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / Ribosomal protein S5 domain 2-type fold
Similarity search - Domain/homology
Chem-KUC / Heat shock protein 75 kDa, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.706 Å
AuthorsDeng, J. / Matts, R. / Peng, S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD) United States
CitationJournal: Eur.J.Med.Chem. / Year: 2023
Title: Elucidation of novel TRAP1-Selective inhibitors that regulate mitochondrial processes.
Authors: Merfeld, T. / Peng, S. / Keegan, B.M. / Crowley, V.M. / Brackett, C.M. / Gutierrez, A. / McCann, N.R. / Reynolds, T.S. / Rhodes, M.C. / Byrd, K.M. / Deng, J. / Matts, R.L. / Blagg, B.S.J.
History
DepositionMar 9, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 16, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)56,0343
Polymers55,2011
Non-polymers8332
Water5,873326
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.070, 68.863, 182.545
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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: 55200.773 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 (E. coli) / References: UniProt: Q12931
#2: Chemical ChemComp-KUC / [5-(4-fluoro-2H-isoindole-2-carbonyl)-2-hydroxyphenyl](5-fluoro-2H-isoindol-2-yl)methanone


Mass: 416.376 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H14F2N2O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 326 / 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: 2.4 Å3/Da / Density % sol: 48.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1M Sodium malonate PH6.0, 12%PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97935 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 3, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97935 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 58263 / % possible obs: 99.7 % / Redundancy: 6 % / CC1/2: 0.975 / Rmerge(I) obs: 0.083 / Net I/σ(I): 25.6
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.376 / Mean I/σ(I) obs: 3.484 / Num. unique obs: 5614 / CC1/2: 0.908

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5HPH

5hph


Resolution: 1.706→38.207 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 21.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2088 1964 3.44 %
Rwork0.1817 55118 -
obs0.1827 57082 97.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 109.23 Å2 / Biso mean: 37.7586 Å2 / Biso min: 17.69 Å2
Refinement stepCycle: final / Resolution: 1.706→38.207 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3556 0 62 327 3945
Biso mean--33.28 44.29 -
Num. residues----440
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063694
X-RAY DIFFRACTIONf_angle_d0.8454982
X-RAY DIFFRACTIONf_chiral_restr0.052539
X-RAY DIFFRACTIONf_plane_restr0.005626
X-RAY DIFFRACTIONf_dihedral_angle_d13.8872208
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.7063-1.7490.3151160.2375316279
1.749-1.79630.22971310.2118370093
1.7963-1.84910.23361350.2079383596
1.8491-1.90880.22361410.1965389997
1.9088-1.9770.23831400.1881389898
1.977-2.05620.21921390.1845394798
2.0562-2.14980.19011410.1884398499
2.1498-2.26310.21691430.19374001100
2.2631-2.40490.23831430.19384029100
2.4049-2.59050.23451440.1981403499
2.5905-2.85110.24031450.19324052100
2.8511-3.26350.23681450.18844109100
3.2635-4.11090.18631470.16324123100
4.1109-38.20.17441540.16824345100
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)
11.4346-0.2859-0.43441.10720.09524.22640.0060.21960.0854-0.50340.0892-0.1265-0.31460.2603-0.10220.5079-0.04050.03090.32350.01590.3053-1.866673.6998119.4854
21.5642-0.40490.29434.5729-0.31052.2308-0.11370.04450.0035-0.09520.1334-0.1297-0.04690.0590.00840.1721-0.0259-0.00190.18030.0080.1775-1.516463.7106125.8048
31.7606-1.4362-0.94192.93981.12013.37130.08690.02990.0899-0.0032-0.10570.1057-0.1998-0.22090.0520.2371-0.03110.01090.2571-0.02090.23829.220837.6663116.9643
41.1799-1.1298-0.96781.82850.7821.8280.0021-0.0496-0.001-0.0010.0013-0.09580.01350.2268-0.01220.1675-0.0291-0.01210.25320.00510.198524.772520.9732102.4069
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 71 through 108 )A71 - 108
2X-RAY DIFFRACTION2chain 'A' and (resid 109 through 297 )A109 - 297
3X-RAY DIFFRACTION3chain 'A' and (resid 298 through 408 )A298 - 408
4X-RAY DIFFRACTION4chain 'A' and (resid 409 through 552 )A409 - 552

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