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- PDB-7aot: The Fk1 domain of FKBP51 in complex with (2R,5S,12R)-12-cyclohexy... -

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Basic information

Entry
Database: PDB / ID: 7aot
TitleThe Fk1 domain of FKBP51 in complex with (2R,5S,12R)-12-cyclohexyl-2-[2-(3,4-dimethoxyphenyl)ethyl]-3,19-dioxa-10,13,16-triazatricyclo[18.3.1.0-5,10]tetracosa- 1(24),20,22-triene-4,11,14,17-tetrone
ComponentsPeptidyl-prolyl cis-trans isomerase FKBP5
KeywordsCHAPERONE / 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 / extracellular exosome / nucleoplasm / membrane / cytosol / cytoplasm
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
Chem-RTQ / Peptidyl-prolyl cis-trans isomerase FKBP5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 0.85 Å
AuthorsVoll, A.M. / Meyners, C. / Heymann, T. / Merz, S. / Purder, P. / Bracher, A. / Hausch, F.
Citation
Journal: Angew.Chem.Int.Ed.Engl. / Year: 2021
Title: Macrocyclic FKBP51 Ligands Define a Transient Binding Mode with Enhanced Selectivity.
Authors: Voll, A.M. / Meyners, C. / Taubert, M.C. / Bajaj, T. / Heymann, T. / Merz, S. / Charalampidou, A. / Kolos, J. / Purder, P.L. / Geiger, T.M. / Wessig, P. / Gassen, N.C. / Bracher, A. / Hausch, F.
#1: Journal: Acta Crystallogr D Biol Crystallogr / 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
DepositionOct 15, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 21, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 9, 2021Group: 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.identifier_ORCID
Revision 1.2Jan 31, 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)14,6622
Polymers14,0261
Non-polymers6361
Water3,927218
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.504, 49.633, 59.903
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-RTQ / (2R,5S,12R)-12-cyclohexyl-2-[2-(3,4-dimethoxyphenyl)ethyl]-3,19-dioxa-10,13,16-triazatricyclo[18.3.1.0-5,10]tetracosa- 1(24),20,22-triene-4,11,14,17-tetrone / (2~{R},5~{S},12~{R})-12-cyclohexyl-2-[2-(3,4-dimethoxyphenyl)ethyl]-3,19-dioxa-10,13,16-triazatricyclo[18.3.1.0^{5,10}]tetracosa-1(24),20,22-triene-4,11,14,17-tetrone


Mass: 635.747 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C35H45N3O8 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 218 / 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: 2.31 Å3/Da / Density % sol: 46.65 % / Mosaicity: 0.05 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 38 % 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 / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.82656 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.82656 Å / Relative weight: 1
ReflectionResolution: 0.85→49.63 Å / Num. obs: 111218 / % possible obs: 97.1 % / Redundancy: 5.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.033 / Rpim(I) all: 0.014 / Rrim(I) all: 0.036 / Net I/σ(I): 22.1 / Num. measured all: 630447
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
0.85-0.863.30.8131347340720.5370.4660.9461.472.4
4.65-49.6360.0349008150.9990.0130.03368.599.6

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation38.22 Å2.9 Å

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Processing

Software
NameVersionClassification
XDSVERSION Oct 15, 2015data reduction
Aimless0.1.27data scaling
MOLREP11.0.05phasing
REFMAC5.8.0071refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdbid 3O5Q

3o5q


Resolution: 0.85→30 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.978 / WRfactor Rfree: 0.1399 / WRfactor Rwork: 0.121 / FOM work R set: 0.9248 / SU B: 0.295 / SU ML: 0.008 / SU R Cruickshank DPI: 0.0126 / SU Rfree: 0.0135 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.013 / ESU R Free: 0.013 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1383 5557 5 %RANDOM
Rwork0.122 ---
obs0.1228 105556 97.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 89.37 Å2 / Biso mean: 12.227 Å2 / Biso min: 4.95 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å2-0 Å2-0 Å2
2---0 Å20 Å2
3---0.03 Å2
Refinement stepCycle: final / Resolution: 0.85→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms963 0 91 223 1277
Biso mean--8.03 23.32 -
Num. residues----127
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.030.021130
X-RAY DIFFRACTIONr_bond_other_d0.0060.021079
X-RAY DIFFRACTIONr_angle_refined_deg2.5222.0171536
X-RAY DIFFRACTIONr_angle_other_deg1.4173.0132521
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8845146
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.48325.36641
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.60315195
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.483152
X-RAY DIFFRACTIONr_chiral_restr0.4530.2160
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0211295
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02237
X-RAY DIFFRACTIONr_rigid_bond_restr6.6132209
X-RAY DIFFRACTIONr_sphericity_free37.523531
X-RAY DIFFRACTIONr_sphericity_bonded9.88252366
LS refinement shellResolution: 0.85→0.872 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 318 -
Rwork0.289 6027 -
all-6345 -
obs--75.59 %

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