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- PDB-9euc: The FK1 domain of FKBP51 in complex with SAFit-analog 23b -

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Basic information

Entry
Database: PDB / ID: 9euc
TitleThe FK1 domain of FKBP51 in complex with SAFit-analog 23b
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: 2.4 Å
AuthorsMeyners, C. / Buffa, V. / Hausch, F.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Federal Ministry for Education and Research Germany
CitationJournal: Chemmedchem / Year: 2024
Title: 1,4-Pyrazolyl-Containing SAFit-Analogues are Selective FKBP51 Inhibitors With Improved Ligand Efficiency and Drug-Like Profile.
Authors: Buffa, V. / Meyners, C. / Sugiarto, W.O. / Bauder, M. / Gaali, S. / Hausch, F.
History
DepositionMar 27, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 12, 2024Provider: repository / Type: Initial release
Revision 1.1Sep 11, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.title / _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
B: Peptidyl-prolyl cis-trans isomerase FKBP5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0634
Polymers28,0082
Non-polymers1,0552
Water36020
1
A: Peptidyl-prolyl cis-trans isomerase FKBP5
hetero molecules


  • defined by author
  • 14.5 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)14,5322
Polymers14,0041
Non-polymers5281
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Peptidyl-prolyl cis-trans isomerase FKBP5
hetero molecules


  • defined by author
  • 14.5 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)14,5322
Polymers14,0041
Non-polymers5281
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.962, 48.962, 195.465
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: GLU / End label comp-ID: GLU / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 13 - 140 / Label seq-ID: 1 - 128

Dom-ID
1
2

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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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.: 2 / 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-A1H7F / (1-ethylpyrazol-4-yl)methyl (2S)-1-[(2S)-2-cyclohexyl-2-(3,4,5-trimethoxyphenyl)ethanoyl]piperidine-2-carboxylate


Mass: 527.652 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C29H41N3O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / 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: 2.41 Å3/Da / Density % sol: 49.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 14% PEG3350, 0.2M sodium thiocyanate, 0.1M HEPES-NaOH pH 7.5 10% ethylene glycol

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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 S 6M / Detector: PIXEL / Date: Mar 18, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.4→42.438 Å / Num. obs: 11402 / % possible obs: 100 % / Redundancy: 10 % / CC1/2: 0.999 / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.025 / Rrim(I) all: 0.058 / Net I/σ(I): 25.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
8.98-42.47.50.0322830.9980.0160.036
2.4-2.499.80.28711810.9630.1390.32

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
autoXDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→42.438 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.899 / SU B: 19.469 / SU ML: 0.218 / Cross valid method: THROUGHOUT / ESU R: 0.444 / ESU R Free: 0.28
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2788 613 5.399 %
Rwork0.2505 10742 -
all0.252 --
obs-11355 99.921 %
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: 46.746 Å2
Baniso -1Baniso -2Baniso -3
1--0.535 Å2-0.268 Å2-0 Å2
2---0.535 Å20 Å2
3---1.737 Å2
Refinement stepCycle: LAST / Resolution: 2.4→42.438 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1722 0 76 20 1818
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0121840
X-RAY DIFFRACTIONr_bond_other_d0.0050.0161672
X-RAY DIFFRACTIONr_angle_refined_deg1.5731.8482504
X-RAY DIFFRACTIONr_angle_other_deg1.2471.7973835
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.4575240
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.03453
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.0110231
X-RAY DIFFRACTIONr_dihedral_angle_6_deg12.0971055
X-RAY DIFFRACTIONr_chiral_restr0.0640.2285
X-RAY DIFFRACTIONr_chiral_restr_other1.4120.232
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022098
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02372
X-RAY DIFFRACTIONr_nbd_refined0.1960.2323
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1960.21510
X-RAY DIFFRACTIONr_nbtor_refined0.1760.2935
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0840.2909
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1610.244
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0510.24
X-RAY DIFFRACTIONr_nbd_other0.1060.216
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1010.22
X-RAY DIFFRACTIONr_mcbond_it2.0422.907981
X-RAY DIFFRACTIONr_mcbond_other2.0412.907981
X-RAY DIFFRACTIONr_mcangle_it3.1225.2091214
X-RAY DIFFRACTIONr_mcangle_other3.1215.211215
X-RAY DIFFRACTIONr_scbond_it2.0492.996859
X-RAY DIFFRACTIONr_scbond_other2.0482.997860
X-RAY DIFFRACTIONr_scangle_it3.195.4741290
X-RAY DIFFRACTIONr_scangle_other3.1895.4741291
X-RAY DIFFRACTIONr_lrange_it4.85427.1881937
X-RAY DIFFRACTIONr_lrange_other4.85527.1931937
X-RAY DIFFRACTIONr_ncsr_local_group_10.0860.053161
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.085750.05008
12AX-RAY DIFFRACTIONLocal ncs0.085750.05008
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
2.4-2.4630.418430.3127800.3188230.8970.9351000.282
2.463-2.530.34320.2597480.2627800.9340.9581000.236
2.53-2.6030.254220.2327690.2337910.9410.9641000.214
2.603-2.6830.273320.2557190.2557510.9520.9631000.23
2.683-2.770.289380.256770.2527150.950.9621000.229
2.77-2.8670.339360.2456870.2497240.9010.95999.86190.23
2.867-2.9750.326250.2646420.2666670.9310.9511000.25
2.975-3.0960.375460.2676380.2746850.9190.94799.8540.258
3.096-3.2320.294340.2745980.2756320.9380.9421000.264
3.232-3.3890.315300.285710.2816010.9020.9481000.279
3.389-3.5710.339490.2635370.2695860.9440.9581000.265
3.571-3.7860.256270.2515330.2515600.9540.9661000.254
3.786-4.0450.219280.2245040.2235320.970.9711000.232
4.045-4.3660.236330.2124460.2144800.9610.97399.79170.225
4.366-4.7780.195330.1994360.1984690.9780.9731000.216
4.778-5.3330.256250.2183980.224240.9570.96899.76420.242
5.333-6.1420.3200.2743620.2763830.9370.95299.73890.298
6.142-7.4840.285210.3032870.3023090.9440.94599.67640.333
7.484-10.4230.301230.2342470.2392710.9330.96699.6310.271
10.423-42.4380.276160.3321630.3281800.9550.93699.44440.403
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)
14.4118-1.5776-0.53254.55431.34914.1523-0.1162-0.63840.54510.10540.339-0.2337-0.06420.3421-0.22280.00660.013-0.01090.31910.02990.14087.89315.837229.1554
23.11950.39540.70532.9926-0.83024.6587-0.0795-0.1335-0.1321-0.0137-0.13830.678-0.1879-0.17360.21790.1715-0.0345-0.08130.15390.02020.2634-9.332316.14543.7712
Refinement TLS groupSelection: ALL

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