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- PDB-8cca: The Fk1 domain of FKBP51 in complex with SAFit1 -

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Basic information

Entry
Database: PDB / ID: 8cca
TitleThe Fk1 domain of FKBP51 in complex with SAFit1
ComponentsPeptidyl-prolyl cis-trans isomerase FKBP5
KeywordsISOMERASE / FKBP51 / SAFit / Inhibitor
Function / homology
Function and homology information


Modulation of host responses by IFN-stimulated genes / response to alcohol / FK506 binding / MECP2 regulates neuronal receptors and channels / : / heat shock protein binding / ESR-mediated signaling / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / response to cocaine / response to bacterium ...Modulation of host responses by IFN-stimulated genes / response to alcohol / FK506 binding / MECP2 regulates neuronal receptors and channels / : / heat shock protein binding / ESR-mediated signaling / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / response to cocaine / response to bacterium / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / protein folding / protein-macromolecule adaptor activity / extracellular exosome / nucleoplasm / membrane / cytoplasm / cytosol
Similarity search - Function
: / Tetratricopeptide repeat / Tetratricopeptide repeat / FKBP-type peptidyl-prolyl cis-trans isomerase / FKBP-type peptidyl-prolyl cis-trans isomerase domain / FKBP-type peptidyl-prolyl cis-trans isomerase domain profile. / TPR repeat region circular profile. / Peptidyl-prolyl cis-trans isomerase domain superfamily / TPR repeat profile. / Tetratricopeptide repeats ...: / Tetratricopeptide repeat / Tetratricopeptide repeat / FKBP-type peptidyl-prolyl cis-trans isomerase / FKBP-type peptidyl-prolyl cis-trans isomerase domain / FKBP-type peptidyl-prolyl cis-trans isomerase domain profile. / TPR repeat region circular profile. / Peptidyl-prolyl cis-trans isomerase domain superfamily / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily
Similarity search - Domain/homology
Chem-GY1 / Peptidyl-prolyl cis-trans isomerase FKBP5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.33 Å
AuthorsMeyners, C. / Knaup, F.H. / Walz, C.M. / Hausch, F.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Federal Ministry for Education and Research Germany
CitationJournal: J.Med.Chem. / Year: 2023
Title: Structure-Based Discovery of a New Selectivity-Enabling Motif for the FK506-Binding Protein 51.
Authors: Knaup, F.H. / Meyners, C. / Sugiarto, W.O. / Wedel, S. / Springer, M. / Walz, C. / Geiger, T.M. / Schmidt, M. / Sisignano, M. / Hausch, F.
History
DepositionJan 27, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 26, 2023Provider: repository / Type: Initial release
Revision 1.1May 10, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Peptidyl-prolyl cis-trans isomerase FKBP5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,7522
Polymers14,0041
Non-polymers7481
Water2,720151
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.625, 48.493, 57.474
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 Peptidyl-prolyl cis-trans isomerase FKBP5 / PPIase FKBP5 / 51 kDa FK506-binding protein / FKBP-51 / 54 kDa progesterone receptor-associated ...PPIase FKBP5 / 51 kDa FK506-binding protein / FKBP-51 / 54 kDa progesterone receptor-associated immunophilin / Androgen-regulated protein 6 / FF1 antigen / FK506-binding protein 5 / FKBP-5 / FKBP54 / p54 / HSP90-binding immunophilin / Rotamase


Mass: 14004.026 Da / Num. of mol.: 1 / Mutation: A19T, C103A, C107I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FKBP5, AIG6, FKBP51 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q13451, peptidylprolyl isomerase
#2: Chemical ChemComp-GY1 / 2-[3-[(1~{R})-1-[(2~{S})-1-[(2~{S})-2-cyclohexyl-2-(3,4,5-trimethoxyphenyl)ethanoyl]piperidin-2-yl]carbonyloxy-3-(3,4-dimethoxyphenyl)propyl]phenoxy]ethanoic acid


Mass: 747.870 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C42H53NO11 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 151 / 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: 2.27 Å3/Da / Density % sol: 45.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 18% PEG3350, 0.1 M HEPES pH 7.5, 0.2 M ammonium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 19, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.33→37.091 Å / Num. obs: 29884 / % possible obs: 99.7 % / Redundancy: 5.8 % / CC1/2: 0.996 / Rmerge(I) obs: 0.051 / Rpim(I) all: 0.034 / Rrim(I) all: 0.062 / Net I/σ(I): 12.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
7.16-37.065.70.0282410.9980.0170.033
1.33-1.354.20.92414610.5850.731.185

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Processing

Software
NameVersionClassification
REFMAC5.8.0403refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.33→37.091 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.965 / SU B: 3.213 / SU ML: 0.056 / Cross valid method: THROUGHOUT / ESU R: 0.058 / ESU R Free: 0.056
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2007 1523 5.105 %
Rwork0.1654 28311 -
all0.167 --
obs-29834 99.586 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 18.489 Å2
Baniso -1Baniso -2Baniso -3
1--0.464 Å2-0 Å2-0 Å2
2---2.141 Å20 Å2
3---2.605 Å2
Refinement stepCycle: LAST / Resolution: 1.33→37.091 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms950 0 54 151 1155
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0121059
X-RAY DIFFRACTIONr_bond_other_d0.0050.017982
X-RAY DIFFRACTIONr_angle_refined_deg1.9161.7161437
X-RAY DIFFRACTIONr_angle_other_deg1.2321.6652271
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.2025133
X-RAY DIFFRACTIONr_dihedral_angle_2_deg3.95353
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.3110155
X-RAY DIFFRACTIONr_dihedral_angle_6_deg17.4541038
X-RAY DIFFRACTIONr_chiral_restr0.0920.2153
X-RAY DIFFRACTIONr_chiral_restr_other1.3580.217
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021211
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02219
X-RAY DIFFRACTIONr_nbd_refined0.190.2181
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1830.2935
X-RAY DIFFRACTIONr_nbtor_refined0.180.2525
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0830.2523
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1350.297
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.4790.25
X-RAY DIFFRACTIONr_nbd_other0.250.244
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1940.215
X-RAY DIFFRACTIONr_mcbond_it1.8092.005529
X-RAY DIFFRACTIONr_mcbond_other1.812.006528
X-RAY DIFFRACTIONr_mcangle_it2.4993.616663
X-RAY DIFFRACTIONr_mcangle_other2.4973.614664
X-RAY DIFFRACTIONr_scbond_it1.7772.133530
X-RAY DIFFRACTIONr_scbond_other1.7752.135531
X-RAY DIFFRACTIONr_scangle_it2.3753.832774
X-RAY DIFFRACTIONr_scangle_other2.3733.833775
X-RAY DIFFRACTIONr_lrange_it4.20324.0321215
X-RAY DIFFRACTIONr_lrange_other3.59522.0111168
X-RAY DIFFRACTIONr_rigid_bond_restr4.99432041
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.33-1.3650.268980.28520210.28421690.9570.95597.69480.286
1.365-1.4020.3181140.26520010.26821170.9560.96999.90550.26
1.402-1.4420.2911030.22219650.22620790.9360.97899.47090.215
1.442-1.4870.2381100.21718900.21820040.9650.98299.80040.202
1.487-1.5350.234920.18618420.18819440.9750.98499.48560.171
1.535-1.5890.191070.15517800.15718920.9790.99199.73570.137
1.589-1.6490.1791080.14417170.14618260.9770.99199.94520.127
1.649-1.7160.182720.14316790.14417620.9790.99199.37570.124
1.716-1.7920.223770.12716380.13117160.970.99299.94170.111
1.792-1.880.177840.12915210.13216110.9830.99199.62760.117
1.88-1.9810.235770.15714600.16115390.9630.98599.870.143
1.981-2.1010.171670.14613920.14814620.9830.98799.79480.139
2.101-2.2450.168780.14212980.14313770.980.97699.92740.138
2.245-2.4250.243660.14612330.1513000.9630.98699.92310.15
2.425-2.6550.171610.14611270.14711910.9820.98699.74810.153
2.655-2.9660.205730.16710120.16910860.9710.98299.90790.183
2.966-3.4220.214420.1729220.1749730.9720.98299.0750.195
3.422-4.1820.188380.1528050.1548440.9770.98699.88150.182
4.182-5.8770.141420.1816120.1786540.9890.9821000.239
5.877-37.0910.368140.2223960.2274120.5650.94399.51460.282

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