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- PDB-5obk: The Fk1 domain of FKBP51 in complex with (1S,5S,6R)-10-((3,5-dich... -

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Basic information

Entry
Database: PDB / ID: 5obk
TitleThe Fk1 domain of FKBP51 in complex with (1S,5S,6R)-10-((3,5-dichlorophenyl)sulfonyl)-5-(hydroxymethyl)-3-(pyridin-2-ylmethyl)-3,10-diazabicyclo[4.3.1]decan-2-one
ComponentsPeptidyl-prolyl cis-trans isomerase FKBP5
KeywordsISOMERASE / Fk-506 binding domain / Hsp90 cochaperone / immunophiline / peptidyl-prolyl isomerase / ligand selectivity
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 / Chitinase A; domain 3 - #40 / Tetratricopeptide repeat 1 / Tetratricopeptide repeat / Chitinase A; domain 3 / 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. ...Tetratricopeptide repeat / Chitinase A; domain 3 - #40 / Tetratricopeptide repeat 1 / Tetratricopeptide repeat / Chitinase A; domain 3 / 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 / Roll / Alpha Beta
Similarity search - Domain/homology
Chem-9QN / Peptidyl-prolyl cis-trans isomerase FKBP5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1 Å
AuthorsPomplun, S. / Sippel, C. / Haehle, A. / Bracher, A. / Hausch, F.
Citation
Journal: J. Med. Chem. / Year: 2018
Title: Chemogenomic Profiling of Human and Microbial FK506-Binding Proteins.
Authors: Pomplun, S. / Sippel, C. / Hahle, A. / Tay, D. / Shima, K. / Klages, A. / Unal, C.M. / Riess, B. / Toh, H.T. / Hansen, G. / Yoon, H.S. / Bracher, A. / Preiser, P. / Rupp, J. / Steinert, M. / Hausch, F.
#1: Journal: ACTA CRYSTALLOGR.,SECT.D / Year: 2011
Title: Structural characterization of the PPIase domain of FKBP51, a cochaperone of human Hsp90
Authors: Bracher, A. / Kozany, C. / Thost, A.K. / Hausch, F.
History
DepositionJun 28, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 4, 2018Provider: repository / Type: Initial release
Revision 1.1May 9, 2018Group: Data collection / 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 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)14,5102
Polymers14,0261
Non-polymers4841
Water4,576254
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.819, 54.915, 56.745
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 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: 14026.077 Da / Num. of mol.: 1 / Fragment: Fk1 domain
Mutation: additional N-terminal sequence GAP, cloning artefact, mutation A19T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FKBP5, AIG6, FKBP51 / Plasmid: pProEx-HtB / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): codon+ RIL / References: UniProt: Q13451, peptidylprolyl isomerase
#2: Chemical ChemComp-9QN / (1~{S},5~{S},6~{R})-10-[3,5-bis(chloranyl)phenyl]sulfonyl-5-(hydroxymethyl)-3-(pyridin-2-ylmethyl)-3,10-diazabicyclo[4.3.1]decan-2-one


Mass: 484.396 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H23Cl2N3O4S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 254 / 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: 2.32 Å3/Da / Density % sol: 47.04 % / Mosaicity: 0 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 30 % PEG-3350, 0.2 M NH4-acetate and 0.1 M HEPES-NaOH pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97857 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 13, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 0.94→39.462 Å / Num. obs: 68012 / % possible obs: 95.4 % / Redundancy: 3.9 % / Rpim(I) all: 0.021 / Rrim(I) all: 0.045 / Rsym value: 0.04 / Net I/av σ(I): 6 / Net I/σ(I): 17.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRpim(I) allRrim(I) allRsym value% possible all
1-1.052.20.2922.60.2080.3620.29274.7
1.05-1.123.50.164.70.0950.1880.1695.6
1.12-1.193.90.10770.060.1240.10799.2
1.19-1.294.30.0838.90.0450.0940.08399.8
1.29-1.414.30.06411.10.0340.0730.06499.5
1.41-1.584.50.04913.60.0260.0560.04999.7
1.58-1.824.40.0415.70.0210.0450.0499.6
1.82-2.234.40.03616.10.0190.0410.03699.5
2.23-3.164.40.03515.50.0180.0390.03599.6
3.16-33.6654.20.03714.30.020.0420.03799.1

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Processing

Software
NameVersionClassification
SCALA3.3.20data scaling
REFMAC5.7.0029refinement
PDB_EXTRACT3.22data extraction
TRUNCATEdata scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdbid 3O5Q

3o5q


Resolution: 1→30 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.979 / SU B: 0.534 / SU ML: 0.013 / SU R Cruickshank DPI: 0.0198 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.02 / ESU R Free: 0.02
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1356 3434 5.1 %RANDOM
Rwork0.119 ---
obs0.1198 64500 95.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 95.55 Å2 / Biso mean: 14.554 Å2 / Biso min: 6.44 Å2
Baniso -1Baniso -2Baniso -3
1--0.45 Å20 Å20 Å2
2---0.2 Å2-0 Å2
3---0.66 Å2
Refinement stepCycle: final / Resolution: 1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms982 0 33 263 1278
Biso mean--12.27 26.49 -
Num. residues----128
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.021129
X-RAY DIFFRACTIONr_bond_other_d0.0030.021090
X-RAY DIFFRACTIONr_angle_refined_deg1.792.0071535
X-RAY DIFFRACTIONr_angle_other_deg0.9693.0072545
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9585147
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.72924.3941
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.61615206
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.861154
X-RAY DIFFRACTIONr_chiral_restr0.1750.2163
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211289
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02244
X-RAY DIFFRACTIONr_rigid_bond_restr2.98932219
X-RAY DIFFRACTIONr_sphericity_free29.378543
X-RAY DIFFRACTIONr_sphericity_bonded10.3752405
LS refinement shellResolution: 1→1.026 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.26 170 -
Rwork0.242 3324 -
all-3494 -
obs--67.66 %

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