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- PDB-9ey3: The FK1 domain of FKBP51 in complex with (3S,11S,11aS)-12-((3,5-d... -

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Basic information

Entry
Database: PDB / ID: 9ey3
TitleThe FK1 domain of FKBP51 in complex with (3S,11S,11aS)-12-((3,5-dichlorophenyl)sulfonyl)-5-oxo-11-vinyldecahydro-1H-6,10-epiminopyrrolo[1,2-a]azonine-3-carboxylic acid
ComponentsPeptidyl-prolyl cis-trans isomerase FKBP5
KeywordsISOMERASE / FKBP51 / Inhibitor / Complex
Function / homology
Function and homology information


FK506 binding / MECP2 regulates neuronal receptors and channels / chaperone-mediated protein folding / heat shock protein binding / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / ESR-mediated signaling / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / response to bacterium / protein folding ...FK506 binding / MECP2 regulates neuronal receptors and channels / chaperone-mediated protein folding / heat shock protein binding / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / ESR-mediated signaling / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / response to bacterium / protein folding / protein-macromolecule adaptor activity / extracellular exosome / nucleoplasm / membrane / cytosol / cytoplasm
Similarity search - Function
: / Tetratricopeptide repeat / Tetratricopeptide repeat / FKBP-type peptidyl-prolyl cis-trans isomerase domain profile. / FKBP-type peptidyl-prolyl cis-trans isomerase domain / FKBP-type peptidyl-prolyl cis-trans isomerase / Peptidyl-prolyl cis-trans isomerase domain superfamily / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats ...: / Tetratricopeptide repeat / Tetratricopeptide repeat / FKBP-type peptidyl-prolyl cis-trans isomerase domain profile. / FKBP-type peptidyl-prolyl cis-trans isomerase domain / FKBP-type peptidyl-prolyl cis-trans isomerase / Peptidyl-prolyl cis-trans isomerase domain superfamily / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily
Similarity search - Domain/homology
: / Peptidyl-prolyl cis-trans isomerase FKBP5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.16 Å
AuthorsMeyners, C. / Krajczy, P. / Hausch, F.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Federal Ministry for Education and Research Germany
CitationJournal: Chemistry / Year: 2024
Title: Structure-Based Design of Ultrapotent Tricyclic Ligands for FK506-Binding Proteins.
Authors: Krajczy, P. / Meyners, C. / Repity, M.L. / Hausch, F.
History
DepositionApr 9, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 12, 2024Provider: repository / Type: Initial release
Revision 1.1Aug 21, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name
Revision 1.2Aug 28, 2024Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)14,4772
Polymers14,0041
Non-polymers4731
Water4,306239
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6700 Å2
Unit cell
Length a, b, c (Å)42.077, 54.553, 56.322
Angle α, β, γ (deg.)90, 90, 90
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-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q13451, peptidylprolyl isomerase
#2: Chemical ChemComp-A1H70 / (1~{S},4~{S},7~{S},8~{S},9~{R})-13-[3,5-bis(chloranyl)phenyl]sulfonyl-8-ethenyl-2-oxidanylidene-3,13-diazatricyclo[7.3.1.0^{3,7}]tridecane-4-carboxylic acid


Mass: 473.370 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H22Cl2N2O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 239 / 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: 2.31 Å3/Da / Density % sol: 46.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 34% PEG3350, 0.2M ammonium acetate, 0.1M HEPES-NaOH pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.885603 Å
DetectorType: DECTRIS EIGER2 X CdTe 16M / Detector: PIXEL / Date: Sep 8, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.885603 Å / Relative weight: 1
ReflectionResolution: 1.16→56.32 Å / Num. obs: 39328 / % possible obs: 86.5 % / Redundancy: 7.1 % / CC1/2: 0.997 / Rmerge(I) obs: 0.064 / Rpim(I) all: 0.038 / Rrim(I) all: 0.074 / Net I/σ(I): 17.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
6.35-56.325.80.0623200.9880.0380.073
1.16-1.1870.18715160.980.1090.217

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.16→33.732 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.962 / SU B: 0.828 / SU ML: 0.018 / Cross valid method: THROUGHOUT / ESU R: 0.037 / ESU R Free: 0.038
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.168 1867 4.753 %
Rwork0.1392 37410 -
all0.14 --
obs-39277 86.149 %
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: 13.515 Å2
Baniso -1Baniso -2Baniso -3
1--0.449 Å2-0 Å20 Å2
2---0.233 Å20 Å2
3---0.683 Å2
Refinement stepCycle: LAST / Resolution: 1.16→33.732 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms958 0 30 239 1227
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0121018
X-RAY DIFFRACTIONr_bond_other_d0.0010.016951
X-RAY DIFFRACTIONr_angle_refined_deg1.8931.8361381
X-RAY DIFFRACTIONr_angle_other_deg0.6511.7562212
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6515128
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.232115
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg0.01252
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.21710169
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.7981038
X-RAY DIFFRACTIONr_chiral_restr0.1170.2153
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021165
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02213
X-RAY DIFFRACTIONr_nbd_refined0.2080.2181
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1980.2899
X-RAY DIFFRACTIONr_nbtor_refined0.1820.2521
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0890.2543
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.270.2150
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2270.29
X-RAY DIFFRACTIONr_nbd_other0.2470.234
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2760.235
X-RAY DIFFRACTIONr_mcbond_it3.6381.057512
X-RAY DIFFRACTIONr_mcbond_other3.5271.053511
X-RAY DIFFRACTIONr_mcangle_it5.0931.904640
X-RAY DIFFRACTIONr_mcangle_other5.0931.905641
X-RAY DIFFRACTIONr_scbond_it5.0951.262506
X-RAY DIFFRACTIONr_scbond_other5.0911.262507
X-RAY DIFFRACTIONr_scangle_it7.1542.218741
X-RAY DIFFRACTIONr_scangle_other7.1492.218742
X-RAY DIFFRACTIONr_lrange_it17.00518.9651258
X-RAY DIFFRACTIONr_lrange_other12.56813.5891155
X-RAY DIFFRACTIONr_rigid_bond_restr3.91131969
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
1.16-1.190.1621170.13424640.13533430.9840.9977.20610.123
1.19-1.2230.1531130.12625260.12732030.9880.99182.39150.117
1.223-1.2580.181280.1225670.12331580.9820.99185.33880.114
1.258-1.2970.1641340.12323180.12630570.9830.99180.20940.118
1.297-1.3390.1591300.11425690.11629590.9840.99291.21320.111
1.339-1.3860.1461160.11121580.11328950.9870.99278.54920.109
1.386-1.4380.1461150.11524920.11727910.9860.99193.40740.116
1.438-1.4970.1411010.10919570.11126760.9870.99376.90580.112
1.497-1.5630.1521310.1120880.11325940.9840.99385.54360.115
1.563-1.640.137940.1122840.11124520.9870.99396.98210.119
1.64-1.7280.1381200.11319340.11523420.9860.99287.70280.124
1.728-1.8330.1441020.11820710.11922410.9870.99196.96560.135
1.833-1.9590.149800.12913840.1321050.9870.9969.54870.149
1.959-2.1150.14650.13716780.13719700.9890.98988.47720.161
2.115-2.3160.189800.13715730.13918120.9790.98891.22520.17
2.316-2.5880.214660.14915480.15216440.970.98698.17520.191
2.588-2.9850.181720.15712880.15814790.980.98591.9540.208
2.985-3.6490.189590.15510800.15612540.9790.98690.82930.2
3.649-5.130.155220.1518770.15110040.9880.98789.54180.214
5.13-33.7320.259220.2415540.2426120.9290.96194.11760.372

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