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- PDB-7u8x: hTRAP1 with inhibitors -

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Basic information

Entry
Database: PDB / ID: 7u8x
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-UJV / Heat shock protein 75 kDa, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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)56,0583
Polymers55,2011
Non-polymers8572
Water5,657314
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)41.758, 68.863, 183.088
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-UJV / [5-(4-fluoro-2H-isoindole-2-carbonyl)-2-hydroxyphenyl](5-methoxy-2H-isoindol-2-yl)methanone


Mass: 428.412 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H17FN2O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 314 / 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: 2.38 Å3/Da / Density % sol: 48.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 1% w/v tryptone, 0.05M HepesNa PH7.0, 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: 1.6→50 Å / Num. obs: 70222 / % possible obs: 99.3 % / Redundancy: 5.8 % / CC1/2: 0.879 / Rmerge(I) obs: 0.101 / Net I/σ(I): 24.028
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.908 / Mean I/σ(I) obs: 1.622 / Num. unique obs: 6727 / CC1/2: 0.629

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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: 1.6→45.772 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 26.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2125 1999 2.85 %
Rwork0.1894 68086 -
obs0.1901 70085 99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 117.87 Å2 / Biso mean: 40.3395 Å2 / Biso min: 20.25 Å2
Refinement stepCycle: final / Resolution: 1.6→45.772 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3568 0 64 316 3948
Biso mean--39.23 46.29 -
Num. residues----440
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063710
X-RAY DIFFRACTIONf_angle_d0.8975004
X-RAY DIFFRACTIONf_chiral_restr0.059540
X-RAY DIFFRACTIONf_plane_restr0.005628
X-RAY DIFFRACTIONf_dihedral_angle_d15.0722217
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.6-1.640.33081320.2982450893
1.64-1.68440.3511390.2806473398
1.6844-1.73390.30751410.2463479499
1.7339-1.78990.28061400.235478999
1.7899-1.85390.26521410.2225480099
1.8539-1.92810.25951430.21134837100
1.9281-2.01590.22111430.19064884100
2.0159-2.12210.21951430.19414861100
2.1221-2.25510.22181420.19144864100
2.2551-2.42920.21941450.19454909100
2.4292-2.67360.22061440.19434923100
2.6736-3.06050.23361450.19294950100
3.0605-3.85550.1821470.17345012100
3.8555-45.70.18891540.17485222100
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)
11.3433-0.39210.12582.43890.95623.17980.1130.16440.0504-0.4023-0.0092-0.1284-0.66760.3315-0.05840.4559-0.0083-0.00740.31110.0290.275639.649108.6363213.1513
23.8291-0.30511.15934.1946-0.57883.5456-0.02260.08790.0971-0.10420.031-0.3010.07640.1708-0.03430.2347-0.01350.00250.16120.01810.204443.015996.8324219.1244
31.55810.3966-1.41057.9171-1.72272.02910.1086-0.07780.0228-0.15850.1946-1.17280.040.8765-0.08220.7553-0.12690.04590.6923-0.09140.484648.823101.5415211.253
41.80570.23560.64756.61580.31533.5934-0.17980.12590.0651-0.33780.22320.0694-0.2904-0.0325-0.03570.2503-0.0217-0.00870.21660.02160.194137.0863103.5469215.0375
52.3094-3.4152-2.06635.19712.37562.9475-0.2748-0.0819-0.2609-0.11620.20410.3460.1615-0.03040.08120.3497-0.0471-0.0250.21460.00280.262341.288583.0315219.1666
62.3319-1.3939-0.9264.01720.84134.8921-0.0952-0.1495-0.06390.08720.0035-0.0056-0.0449-0.25490.06490.2682-0.03690.01090.2598-0.0410.191351.806268.6822213.2793
73.282-0.4522-0.44422.9034-1.89534.64290.18430.9666-1.2828-0.2367-0.24080.77070.3323-0.48150.05060.4644-0.17750.09631.07-0.62661.298344.322963.1673197.2345
86.8783-3.4683-4.5945.5294-0.64355.40990.33930.7760.0154-0.4496-0.34880.12170.2923-0.7801-0.11290.46340.0184-0.01810.3578-0.01960.284747.347380.5452205.1622
93.5291-0.8902-1.11815.01931.69084.2440.14490.10120.3664-0.2928-0.12380.1283-0.5441-0.08550.02750.30680.0074-0.01020.23660.01240.214952.447975.1843201.978
104.8773-3.09020.68273.2775-2.69065.76420.05140.02570.36840.056-0.1235-0.4219-0.39690.29350.03420.293-0.0563-0.00830.2606-0.04090.203461.423370.6185202.7577
114.5991-0.2274-2.59944.3545-0.95648.5757-0.00140.0175-0.0057-0.07150.06140.06290.2209-0.1431-0.02480.2273-0.0182-0.01650.1987-0.05620.190958.470659.758196.9639
122.413-1.1906-0.99232.62240.14172.45060.0219-0.1009-0.1088-0.0281-0.063-0.06280.15530.23080.02250.2304-0.0110.00570.2933-0.00060.192269.621650.1354190.7952
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 70:103)A70 - 103
2X-RAY DIFFRACTION2(chain A and resid 104:170)A104 - 170
3X-RAY DIFFRACTION3(chain A and resid 171:204)A171 - 204
4X-RAY DIFFRACTION4(chain A and resid 205:275)A205 - 275
5X-RAY DIFFRACTION5(chain A and resid 276:302)A276 - 302
6X-RAY DIFFRACTION6(chain A and resid 303:350)A303 - 350
7X-RAY DIFFRACTION7(chain A and resid 351:362)A351 - 362
8X-RAY DIFFRACTION8(chain A and resid 363:379)A363 - 379
9X-RAY DIFFRACTION9(chain A and resid 380:406)A380 - 406
10X-RAY DIFFRACTION10(chain A and resid 407:434)A407 - 434
11X-RAY DIFFRACTION11(chain A and resid 435:459)A435 - 459
12X-RAY DIFFRACTION12(chain A and resid 460:552)A460 - 552

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