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- PDB-9eu8: The FK1 domain of FKBP51 in complex with SAFit-analog 15h -

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Basic information

Entry
Database: PDB / ID: 9eu8
TitleThe FK1 domain of FKBP51 in complex with SAFit-analog 15h
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: 2.3 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)29,0694
Polymers28,0082
Non-polymers1,0612
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)14,5352
Polymers14,0041
Non-polymers5311
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)14,5352
Polymers14,0041
Non-polymers5311
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.293, 48.293, 186.026
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: GLU / Beg label comp-ID: GLU / End auth comp-ID: LYS / End label comp-ID: LYS / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 20 - 138 / Label seq-ID: 8 - 126

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-A1H7B / (4-methyl-1,3-thiazol-5-yl)methyl (2S)-1-[(2S)-2-cyclohexyl-2-(3,4,5-trimethoxyphenyl)ethanoyl]piperidine-2-carboxylate


Mass: 530.676 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C28H38N2O6S / 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: 2.24 Å3/Da / Density % sol: 44.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 12% 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: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 24, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→46.51 Å / Num. obs: 11940 / % possible obs: 100 % / Redundancy: 9.6 % / CC1/2: 0.995 / Rmerge(I) obs: 0.144 / Rpim(I) all: 0.069 / Rrim(I) all: 0.16 / Net I/σ(I): 7.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
8.91-46.5180.1112690.9940.0520.123
2.3-2.3810.11.28411300.6960.6111.424

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→41.858 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.94 / SU B: 28.821 / SU ML: 0.297 / Cross valid method: THROUGHOUT / ESU R: 0.397 / ESU R Free: 0.251
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2595 610 5.14 %
Rwork0.2328 11258 -
all0.234 --
obs-11868 99.739 %
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: 54.53 Å2
Baniso -1Baniso -2Baniso -3
1--2.582 Å2-1.291 Å2-0 Å2
2---2.582 Å20 Å2
3---8.377 Å2
Refinement stepCycle: LAST / Resolution: 2.3→41.858 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1818 0 74 20 1912
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0121937
X-RAY DIFFRACTIONr_bond_other_d0.0030.0161806
X-RAY DIFFRACTIONr_angle_refined_deg1.9021.8642623
X-RAY DIFFRACTIONr_angle_other_deg0.7721.814166
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.6475246
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.8254
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.47510288
X-RAY DIFFRACTIONr_dihedral_angle_6_deg13.0021066
X-RAY DIFFRACTIONr_chiral_restr0.0850.2288
X-RAY DIFFRACTIONr_chiral_restr_other0.8750.228
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022191
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02389
X-RAY DIFFRACTIONr_nbd_refined0.2040.2328
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1980.21707
X-RAY DIFFRACTIONr_nbtor_refined0.1810.2953
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0840.21005
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1470.244
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1730.210
X-RAY DIFFRACTIONr_nbd_other0.1470.263
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.150.22
X-RAY DIFFRACTIONr_mcbond_it3.5393.764996
X-RAY DIFFRACTIONr_mcbond_other3.5393.764996
X-RAY DIFFRACTIONr_mcangle_it5.4646.7551238
X-RAY DIFFRACTIONr_mcangle_other5.4626.7541239
X-RAY DIFFRACTIONr_scbond_it3.0453.755941
X-RAY DIFFRACTIONr_scbond_other3.0443.755942
X-RAY DIFFRACTIONr_scangle_it4.8056.8531385
X-RAY DIFFRACTIONr_scangle_other4.8036.8521386
X-RAY DIFFRACTIONr_lrange_it7.19433.9142034
X-RAY DIFFRACTIONr_lrange_other7.19233.912035
X-RAY DIFFRACTIONr_ncsr_local_group_10.1120.053244
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.111750.05008
12AX-RAY DIFFRACTIONLocal ncs0.111750.05008
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
2.3-2.360.368340.3827910.3828260.8150.85199.87890.383
2.36-2.4240.296400.3658070.3628480.8760.87999.88210.367
2.424-2.4940.431310.3047590.3087910.8520.9299.87360.302
2.494-2.5710.295500.277470.2717990.9250.94699.74970.267
2.571-2.6550.319570.3087190.3097760.9270.9321000.307
2.655-2.7470.437350.2986900.3047260.8830.93299.86230.292
2.747-2.8510.24260.2897180.2877470.9570.93799.59840.286
2.851-2.9660.293280.256520.2526810.9350.95499.85320.245
2.966-3.0980.299380.2466270.2496670.940.95899.70010.243
3.098-3.2480.269370.256140.2516510.930.9571000.248
3.248-3.4220.301380.2485690.2516080.9480.95999.83550.249
3.422-3.6290.282450.2425420.2465900.9510.96499.49150.247
3.629-3.8770.331280.2255070.235370.9230.96999.62760.235
3.877-4.1850.36210.1965060.2025280.9310.97699.81060.214
4.185-4.5790.232280.1444400.1484720.9720.98699.15250.166
4.579-5.1120.162260.1534200.1534480.9790.98699.55360.174
5.112-5.8890.123150.1883740.1853890.9890.9781000.219
5.889-7.1770.184140.2473310.2443480.9790.96399.13790.281
7.177-10.0030.285130.2282650.2312790.9450.96599.64160.283
10.003-41.8580.17960.3021800.2951870.9860.92899.46520.38
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)
16.2192-0.0478-0.29163.340.54183.14320.10240.060.13160.1339-0.01640.0248-0.23650.1538-0.0860.183-0.1003-0.03040.08370.01560.0166-8.924416.5598-2.9532
23.2911-0.0770.55314.20160.98892.7728-0.0601-0.145-0.3268-0.24340.2855-0.11540.167-0.0508-0.22540.148-0.14930.02640.3794-0.08920.0745-18.54990.3325-27.1315
Refinement TLS groupSelection: ALL

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