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- PDB-7c05: Crystal structure of human Trap1 with DN203495 -

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Basic information

Entry
Database: PDB / ID: 7c05
TitleCrystal structure of human Trap1 with DN203495
ComponentsHeat shock protein 75 kDa, mitochondrial
KeywordsCHAPERONE / TRAP1 / selectivity / mitochondria / Hsp90 / Anticancer / Drug
Function / homology
Function and homology information


translational attenuation / negative regulation of cellular respiration / Citric acid cycle (TCA cycle) / Respiratory electron transport / tumor necrosis factor receptor binding / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / negative regulation of reactive oxygen species biosynthetic process / chaperone-mediated protein folding / cell periphery / ATP-dependent protein folding chaperone ...translational attenuation / negative regulation of cellular respiration / Citric acid cycle (TCA cycle) / Respiratory electron transport / tumor necrosis factor receptor binding / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / negative regulation of reactive oxygen species biosynthetic process / chaperone-mediated protein folding / 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-FE6 / Heat shock protein 75 kDa, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.59 Å
AuthorsKim, D. / Kim, D. / Kim, S.Y. / Lee, J.H. / Kang, B.H. / Kang, S. / Lee, C.
CitationJournal: Bioorg.Chem. / Year: 2020
Title: Development of pyrazolo[3,4-d]pyrimidine-6-amine-based TRAP1 inhibitors that demonstrate in vivo anticancer activity in mouse xenograft models.
Authors: Kim, D. / Kim, S.Y. / Kim, D. / Yoon, N.G. / Yun, J. / Hong, K.B. / Lee, C. / Lee, J.H. / Kang, B.H. / Kang, S.
History
DepositionApr 30, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 8, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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)57,7792
Polymers57,4221
Non-polymers3571
Water1,20767
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 area22360 Å2
Unit cell
Length a, b, c (Å)69.891, 69.891, 255.777
Angle α, β, γ (deg.)90.0, 90.0, 90.0
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 / 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-FE6 / 1-[(4-bromanyl-2-fluoranyl-phenyl)methyl]-4-chloranyl-pyrazolo[3,4-d]pyrimidin-6-amine


Mass: 356.581 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H8BrClFN5 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / 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: 2.72 Å3/Da / Density % sol: 54.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.76
Details: 0.1M Cacodylate pH 6.76, 0.1M Ca-acetate, 14% PEG 20000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 0.9794 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 7, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.59→50 Å / Num. obs: 20501 / % possible obs: 99.3 % / Redundancy: 10.5 % / Biso Wilson estimate: 48.8940709925 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 21.1
Reflection shellResolution: 2.6→2.64 Å / Rmerge(I) obs: 0.521 / Num. unique obs: 20501

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Processing

Software
NameVersionClassification
HKL-2000data processing
PHENIX1.9_1692refinement
Cootmodel building
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5Y3N

5y3n


Resolution: 2.59→49.42 Å / SU ML: 0.357867561877 / Cross valid method: FREE R-VALUE / σ(F): 1.43 / Phase error: 26.5605219153
RfactorNum. reflection% reflection
Rfree0.2829 1023 5.00122219506 %
Rwork0.2219 --
obs0.224990276014 20455 98.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 65.1610402535 Å2
Refinement stepCycle: LAST / Resolution: 2.59→49.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3527 0 20 67 3614
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002938960061773618
X-RAY DIFFRACTIONf_angle_d0.5576989368574873
X-RAY DIFFRACTIONf_chiral_restr0.0209146450895534
X-RAY DIFFRACTIONf_plane_restr0.00183087528547616
X-RAY DIFFRACTIONf_dihedral_angle_d11.80697942331359
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.72740.3357767768231360.2716170179032582X-RAY DIFFRACTION94.9353824659
2.7274-2.89820.3082951268311440.2549702719372734X-RAY DIFFRACTION99.4127806563
2.8982-3.1220.2669251305341440.2391764755972738X-RAY DIFFRACTION99.6542185339
3.122-3.43610.2784277111531440.2276858804112755X-RAY DIFFRACTION99.6905089409
3.4361-3.93310.2581083964111470.2063742150232772X-RAY DIFFRACTION98.9156218231
3.9331-4.95460.2593075473911490.1982082670922837X-RAY DIFFRACTION99.5665221741
4.9546-49.420.3110156644571590.2255322783193014X-RAY DIFFRACTION99.6545226131
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)
12.25597888753-0.254493974711-0.2219770537390.3692274359360.2832387343841.4573710733-0.09361130963750.4553353926240.471859501784-0.316155464488-0.02487396900010.8863774519350.1234185145720.2423341624060.1396108147470.733098460189-0.0319013831221-0.3008223108620.285462180230.03290378925250.64680271409685.72727794620.6329366701722.1756150496
20.665466009503-0.3015641038050.1400101048081.520739389650.4260097821660.260740614339-0.02450278931360.1754792246650.000178396339398-0.3717340799820.08644853423130.278786186207-0.0483460291037-0.0553861721897-0.008494983557720.770707499778-0.0513901423157-0.2942678492190.2569077842540.01965021941290.40999382111582.392912948511.304446506520.691528405
31.02061136224-0.1113071166580.7794256831720.1880146120020.1838075001711.30690619173-0.00210853326767-0.0837301340313-0.1340532255640.04157570132330.1123156211780.1656340800060.117771620764-0.0735280859028-0.1471321825580.609253998867-0.00126118353053-0.3015442774720.4062725617430.1907431410050.58694815279367.272562086737.524373127219.2651957486
40.624578384652-0.1534093258050.04904309894970.3702120341370.02187088107080.584640181261-0.0135556893943-0.09311752111840.02044705545620.1664651820410.242883928610.310592965604-0.389985075051-0.584913808493-0.227535130920.5934286568260.0970865279622-0.1337256175370.6066304276970.375231618460.78904119857948.766819343758.830518693911.397582394
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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