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- PDB-7u8u: hTRAP1 with inhibitors -

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Basic information

Entry
Database: PDB / ID: 7u8u
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-UJY / Heat shock protein 75 kDa, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.065 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
B: Heat shock protein 75 kDa, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,8034
Polymers110,4022
Non-polymers1,4022
Water0
1
A: Heat shock protein 75 kDa, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,9022
Polymers55,2011
Non-polymers7011
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Heat shock protein 75 kDa, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,9022
Polymers55,2011
Non-polymers7011
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)66.368, 118.587, 69.393
Angle α, β, γ (deg.)90.000, 90.870, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resseq 70:74 or (resid 75 and (name...
21(chain B and (resseq 70:74 or (resid 75 and (name...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROILEILE(chain A and (resseq 70:74 or (resid 75 and (name...AA70 - 741 - 5
12ILEILEILEILE(chain A and (resseq 70:74 or (resid 75 and (name...AA756
13PROPROLEULEU(chain A and (resseq 70:74 or (resid 75 and (name...AA70 - 5471 - 478
14PROPROLEULEU(chain A and (resseq 70:74 or (resid 75 and (name...AA70 - 5471 - 478
15PROPROLEULEU(chain A and (resseq 70:74 or (resid 75 and (name...AA70 - 5471 - 478
16PROPROLEULEU(chain A and (resseq 70:74 or (resid 75 and (name...AA70 - 5471 - 478
17PROPROLEULEU(chain A and (resseq 70:74 or (resid 75 and (name...AA70 - 5471 - 478
18PROPROLEULEU(chain A and (resseq 70:74 or (resid 75 and (name...AA70 - 5471 - 478
21PROPROILEILE(chain B and (resseq 70:74 or (resid 75 and (name...BB70 - 741 - 5
22ILEILEILEILE(chain B and (resseq 70:74 or (resid 75 and (name...BB756
23PROPROGLUGLU(chain B and (resseq 70:74 or (resid 75 and (name...BB70 - 5511 - 482
24PROPROGLUGLU(chain B and (resseq 70:74 or (resid 75 and (name...BB70 - 5511 - 482
25PROPROGLUGLU(chain B and (resseq 70:74 or (resid 75 and (name...BB70 - 5511 - 482
26PROPROGLUGLU(chain B and (resseq 70:74 or (resid 75 and (name...BB70 - 5511 - 482
27PROPROGLUGLU(chain B and (resseq 70:74 or (resid 75 and (name...BB70 - 5511 - 482
28PROPROGLUGLU(chain B and (resseq 70:74 or (resid 75 and (name...BB70 - 5511 - 482

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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.: 2
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-UJY / [2-hydroxy-5-(2H-isoindole-2-carbonyl)phenyl]{5-[3-(triphenyl-lambda~5~-phosphanyl)propoxy]-2H-isoindol-2-yl}methanone


Mass: 700.760 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C45H37N2O4P / 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: 2.47 Å3/Da / Density % sol: 50.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1M Hepes PH7.0, 15%PEG20K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97951 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 4, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97951 Å / Relative weight: 1
ReflectionResolution: 3.06→50 Å / Num. obs: 19398 / % possible obs: 98.6 % / Redundancy: 6 % / CC1/2: 0.963 / Rmerge(I) obs: 0.238 / Net I/σ(I): 11.211
Reflection shellResolution: 3.06→3.21 Å / Redundancy: 4.6 % / Rmerge(I) obs: 1.569 / Mean I/σ(I) obs: 1.111 / Num. unique obs: 1910 / CC1/2: 0.606 / % possible all: 96

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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: 3.065→48.324 Å / SU ML: 0.5 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 39.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3115 1824 10.03 %
Rwork0.2202 16361 -
obs0.2294 18185 89.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 207.84 Å2 / Biso mean: 101.6096 Å2 / Biso min: 22.98 Å2
Refinement stepCycle: final / Resolution: 3.065→48.324 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6737 0 104 0 6841
Biso mean--105.07 --
Num. residues----831
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.016984
X-RAY DIFFRACTIONf_angle_d1.5429408
X-RAY DIFFRACTIONf_chiral_restr0.081024
X-RAY DIFFRACTIONf_plane_restr0.011179
X-RAY DIFFRACTIONf_dihedral_angle_d12.0784194
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3199X-RAY DIFFRACTION9.541TORSIONAL
12B3199X-RAY DIFFRACTION9.541TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.065-3.14740.4468730.309563846
3.1474-3.240.40611210.3145111480
3.24-3.34450.43961240.3139120586
3.3445-3.4640.3981420.282122988
3.464-3.60270.35561330.251127391
3.6027-3.76660.29541510.239127893
3.7666-3.96510.31391620.2271131595
3.9651-4.21330.33151420.224135997
4.2133-4.53840.31261640.1929137598
4.5384-4.99470.27821500.1792136297
4.9947-5.71650.2931600.2013139599
5.7165-7.19840.28781430.2449141199
7.1984-48.30.27931590.1903140798
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)
15.91390.45130.22883.8799-0.766.51990.2104-0.8522-0.50520.8216-0.12440.4491.4046-1.17990.11691.2726-0.04610.18870.79540.19340.5764-13.486421.6175-4.7569
25.028-0.23750.95454.5612-0.16438.226-0.04820.0696-0.37710.5257-0.07790.09050.7317-0.39310.1730.6953-0.01690.17140.580.00310.3724-11.122925.9048-11.5585
35.44821.51833.67730.64711.21884.29230.146-0.09220.14080.00030.01840.0554-0.1350.2555-0.01850.8055-0.04860.17340.484-0.12060.5284-24.675824.1539-41.0795
46.61870.8172.1583.9141.19445.55780.30811.3574-0.4139-1.3379-0.17140.35060.410.2031-0.02981.07690.0209-0.02440.8162-0.18930.741-45.901514.8596-62.5832
54.273-0.8397-1.00023.8841-0.29094.54410.31311.17841.0212-0.2242-0.38380.4758-0.0858-1.0508-0.05840.70940.1984-0.07931.14620.04460.8792-1.7724-10.8724-30.6175
66.29661.7304-2.95288.8328-1.3786.889-0.6458-0.0081-0.39130.1120.48680.09990.3209-0.33360.15920.5970.1622-0.01250.6573-0.11410.365-0.6181-22.4154-16.1746
75.71390.5202-4.02868.39290.0592.8445-0.2670.51510.47230.30030.23780.1601-0.6811-0.7883-0.00490.89920.28820.05160.81750.04830.55380.4173-15.3269-26.223
83.9358-2.3952-0.89776.22151.62375.75930.40060.45810.6478-0.72710.3676-0.2313-0.879-0.2359-0.43291.57840.720.09281.02530.05040.43820.6854-11.4306-29.1701
95.7958-0.0806-5.83660.1044-0.32998.02990.7622-0.81421.05660.4819-0.23140.3317-1.0618-0.2001-0.43221.09430.2642-0.03690.87040.00110.64783.5947-10.2953-9.1001
107.778-0.4349-2.26347.57820.52819.82850.0935-1.1604-0.01150.5203-0.145-0.56560.50760.93170.34760.57680.2818-0.06220.866-0.04680.5171-7.8652-18.18837.0927
116.8651-3.0231-2.64859.86611.88115.7459-0.17430.4585-0.0534-0.74280.1621-0.08180.87610.85650.02750.76250.24490.06571.0169-0.0020.5014-14.1145-12.92391.4594
124.8105-0.6239-0.63095.33362.97498.5068-0.26670.65090.271-0.25810.2268-0.485-0.28840.4681-0.16261.03030.1761-0.02830.5078-0.06490.783-20.0119-7.39540.6738
134.18590.4307-6.45593.12651.04522.352-0.3140.069-0.46650.31820.23120.25450.4996-0.38220.090.83760.19560.01050.79740.00210.7158-28.7567-10.376919.1533
144.3141-2.55020.87053.15231.66619.1549-0.1173-1.2999-0.27940.90570.41990.68140.3436-0.6891-0.45611.53150.12630.461.16440.17410.9818-35.6497-0.357935.3163
157.26011.5007-3.20247.22490.23074.64560.2760.6047-0.73130.4689-0.13110.58740.027-1.2087-0.14210.6316-0.10030.10370.7473-0.0120.7372-40.2297-2.558621.0383
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 70 through 110 )A70 - 110
2X-RAY DIFFRACTION2chain 'A' and (resid 111 through 277 )A111 - 277
3X-RAY DIFFRACTION3chain 'A' and (resid 278 through 454 )A278 - 454
4X-RAY DIFFRACTION4chain 'A' and (resid 455 through 547 )A455 - 547
5X-RAY DIFFRACTION5chain 'B' and (resid 70 through 110 )B70 - 110
6X-RAY DIFFRACTION6chain 'B' and (resid 111 through 147 )B111 - 147
7X-RAY DIFFRACTION7chain 'B' and (resid 148 through 203 )B148 - 203
8X-RAY DIFFRACTION8chain 'B' and (resid 204 through 266 )B204 - 266
9X-RAY DIFFRACTION9chain 'B' and (resid 267 through 292 )B267 - 292
10X-RAY DIFFRACTION10chain 'B' and (resid 293 through 333 )B293 - 333
11X-RAY DIFFRACTION11chain 'B' and (resid 334 through 373 )B334 - 373
12X-RAY DIFFRACTION12chain 'B' and (resid 374 through 413 )B374 - 413
13X-RAY DIFFRACTION13chain 'B' and (resid 414 through 499 )B414 - 499
14X-RAY DIFFRACTION14chain 'B' and (resid 500 through 531 )B500 - 531
15X-RAY DIFFRACTION15chain 'B' and (resid 532 through 551 )B532 - 551

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