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- PDB-9eue: The FK1 domain of FKBP51 in complex with SAFit-analog 23a -

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Basic information

Entry
Database: PDB / ID: 9eue
TitleThe FK1 domain of FKBP51 in complex with SAFit-analog 23a
ComponentsPeptidyl-prolyl cis-trans isomerase FKBP5
KeywordsISOMERASE / FKBP51 / Inhibitor / Complex
Function / homology
Function and homology information


FK506 binding / chaperone-mediated protein folding / MECP2 regulates neuronal receptors and channels / 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 / chaperone-mediated protein folding / MECP2 regulates neuronal receptors and channels / 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 / cytoplasm / cytosol
Similarity search - Function
Tetratricopeptide repeat / Tetratricopeptide repeat 1 / 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 1 / 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 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

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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)29,0354
Polymers28,0082
Non-polymers1,0272
Water1,51384
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)14,5182
Polymers14,0041
Non-polymers5141
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)14,5182
Polymers14,0041
Non-polymers5141
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.027, 49.027, 196.819
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-A1H68 / (1-methylpyrazol-4-yl)methyl (2S)-1-[(2S)-2-cyclohexyl-2-(3,4,5-trimethoxyphenyl)ethanoyl]piperidine-2-carboxylate


Mass: 513.626 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C28H39N3O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / 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: 2.44 Å3/Da / Density % sol: 49.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 18% PEG3350, 0.2M ammonium acetate, 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 15, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2→42.495 Å / Num. obs: 19549 / % possible obs: 100 % / Redundancy: 11.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.038 / Rrim(I) all: 0.096 / Net I/σ(I): 14.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
8.94-42.468.50.0472870.9990.0210.052
2-2.0511.10.91614220.8260.4121.006

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
autoXDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→42.495 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.931 / SU B: 9.777 / SU ML: 0.137 / Cross valid method: THROUGHOUT / ESU R: 0.189 / ESU R Free: 0.168
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2502 963 4.942 %
Rwork0.2117 18522 -
all0.214 --
obs-19485 99.933 %
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: 40.664 Å2
Baniso -1Baniso -2Baniso -3
1--0.718 Å2-0.359 Å2-0 Å2
2---0.718 Å20 Å2
3---2.328 Å2
Refinement stepCycle: LAST / Resolution: 2→42.495 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1856 0 74 84 2014
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0121976
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161845
X-RAY DIFFRACTIONr_angle_refined_deg1.841.8182681
X-RAY DIFFRACTIONr_angle_other_deg0.6321.734247
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.5625254
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.42914.37516
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.45210280
X-RAY DIFFRACTIONr_dihedral_angle_6_deg13.7791063
X-RAY DIFFRACTIONr_chiral_restr0.0910.2298
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022250
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02400
X-RAY DIFFRACTIONr_nbd_refined0.1940.2349
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1930.21648
X-RAY DIFFRACTIONr_nbtor_refined0.1780.2977
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0820.2977
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1810.286
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0080.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1550.29
X-RAY DIFFRACTIONr_nbd_other0.0970.228
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1220.25
X-RAY DIFFRACTIONr_mcbond_it3.0122.8421022
X-RAY DIFFRACTIONr_mcbond_other2.9972.8411022
X-RAY DIFFRACTIONr_mcangle_it4.0955.1021274
X-RAY DIFFRACTIONr_mcangle_other4.0975.1031275
X-RAY DIFFRACTIONr_scbond_it3.0392.893954
X-RAY DIFFRACTIONr_scbond_other3.0382.893955
X-RAY DIFFRACTIONr_scangle_it4.3435.2571407
X-RAY DIFFRACTIONr_scangle_other4.3415.2571408
X-RAY DIFFRACTIONr_lrange_it6.14326.8792125
X-RAY DIFFRACTIONr_lrange_other6.14426.6852112
X-RAY DIFFRACTIONr_ncsr_local_group_10.0970.053507
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.097410.05008
12AX-RAY DIFFRACTIONLocal ncs0.097410.05008
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
2-2.0520.297730.25513400.25714140.9290.95299.92930.248
2.052-2.1080.363480.23613010.2413490.8960.961000.224
2.108-2.1690.314600.23612840.2413440.9390.9611000.219
2.169-2.2350.26630.21812700.2213330.9610.9671000.2
2.235-2.3090.262600.21611550.21812150.9530.9691000.197
2.309-2.3890.264970.21811190.22212160.9540.9681000.199
2.389-2.4790.265660.22711270.22911940.9620.96799.91630.208
2.479-2.580.25660.21610880.21811540.9580.971000.201
2.58-2.6940.283730.22810070.23210800.9540.9651000.212
2.694-2.8250.239260.24110230.24110490.9540.9611000.227
2.825-2.9770.28390.2399630.2410020.9450.9621000.229
2.977-3.1570.303360.2319290.2349650.9330.9641000.227
3.157-3.3740.246570.2438290.2438870.9580.96199.88730.246
3.374-3.6420.257440.2228010.2248450.9660.9721000.226
3.642-3.9870.235330.1927610.1937940.9790.9811000.2
3.987-4.4520.213450.1636850.1667310.9760.98599.86320.18
4.452-5.1320.165310.1565930.1576250.9850.98699.840.181
5.132-6.2620.246140.1955460.1965600.9540.9791000.217
6.262-8.7620.305150.2124340.2154510.9570.97699.55650.244
8.762-42.4950.271170.2592670.262890.9550.93498.26990.304
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)
14.8877-0.58921.24692.92740.11582.82950.35780.3553-0.4741-0.2904-0.19850.25480.22340.1589-0.15930.14770.0952-0.02430.0653-0.02970.0716-9.9729-14.9065-29.7673
23.0136-0.275-0.25923.06020.30613.89090.0771-0.08520.5926-0.1022-0.15160.3376-0.3296-0.12530.07450.0953-0.01020.01290.0223-0.04610.1738-18.53950.3143-4.0938
Refinement TLS groupSelection: ALL

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