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- PDB-7etu: The FK1 domain of FKBP51 in complex with peptide-inhibitor hit SFPFT -

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Basic information

Entry
Database: PDB / ID: 7etu
TitleThe FK1 domain of FKBP51 in complex with peptide-inhibitor hit SFPFT
Components
  • Peptidyl-prolyl cis-trans isomerase FKBP5
  • peptide-inhibitor hit
KeywordsISOMERASE
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)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.39 Å
AuthorsHan, J.T. / Zhu, Y.C. / Pan, D.B. / Xue, H.X. / Wang, S. / Liu, H.X. / He, Y.X. / Yao, X.J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)21775060 China
CitationJournal: Comput Struct Biotechnol J / Year: 2021
Title: Discovery of pentapeptide-inhibitor hits targeting FKBP51 by combining computational modeling and X-ray crystallography.
Authors: Han, J.T. / Zhu, Y. / Pan, D.B. / Xue, H.X. / Wang, S. / Peng, Y. / Liu, H. / He, Y.X. / Yao, X.
History
DepositionMay 14, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 23, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: peptide-inhibitor hit
A: Peptidyl-prolyl cis-trans isomerase FKBP5


Theoretical massNumber of molelcules
Total (without water)14,6242
Polymers14,6242
Non-polymers00
Water3,369187
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area740 Å2
ΔGint-6 kcal/mol
Surface area6850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.326, 54.425, 56.319
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/peptide peptide-inhibitor hit


Mass: 597.659 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Protein Peptidyl-prolyl cis-trans isomerase FKBP5 / PPIase FKBP5 / 51 kDa FK506-binding protein / 51 kDa FKBP / FKBP-51 / 54 kDa progesterone receptor- ...PPIase FKBP5 / 51 kDa FK506-binding protein / 51 kDa FKBP / 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: 14026.077 Da / Num. of mol.: 1 / Mutation: A19T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FKBP5, AIG6, FKBP51 / Production host: Escherichia coli (E. coli) / References: UniProt: Q13451, peptidylprolyl isomerase
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 187 / Source method: isolated from a natural source / Formula: H2O

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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: 2.22 Å3/Da / Density % sol: 44.54 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN I/F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 30%-36% PEG 3350, 0.2 M Ammonium Acetate and 0.1 M HEPES pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 6, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.39→50 Å / Num. obs: 26679 / % possible obs: 99.2 % / Redundancy: 12 % / Rpim(I) all: 0.026 / Net I/σ(I): 55.14
Reflection shellResolution: 1.39→1.41 Å / Num. unique obs: 1265 / Rpim(I) all: 0.055

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3O5R

3o5r


Resolution: 1.39→28.18 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.941 / SU B: 0.737 / SU ML: 0.031 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.057 / ESU R Free: 0.06 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1955 1255 4.7 %RANDOM
Rwork0.1686 ---
obs0.1698 25371 99.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 49.33 Å2 / Biso mean: 10.95 Å2 / Biso min: 4.42 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å2-0 Å2
2---0.01 Å20 Å2
3----0 Å2
Refinement stepCycle: final / Resolution: 1.39→28.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms996 0 0 187 1183
Biso mean---18.97 -
Num. residues----132
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0141018
X-RAY DIFFRACTIONr_bond_other_d0.0010.017929
X-RAY DIFFRACTIONr_angle_refined_deg1.8031.6531372
X-RAY DIFFRACTIONr_angle_other_deg1.0731.6532172
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.555130
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.8123.63644
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.64615169
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.307153
X-RAY DIFFRACTIONr_chiral_restr0.0990.2131
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021142
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02194
LS refinement shellResolution: 1.391→1.427 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.192 80 -
Rwork0.166 1816 -
all-1896 -
obs--97.78 %

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