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- PDB-4w9q: 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: 4w9q
TitleThe Fk1 domain of FKBP51 in complex with (1S,5S,6R)-10-[(3,5-dichlorophenyl)sulfonyl]-3-[2-(3,4-dimethoxyphenoxy)ethyl]-5-ethyl-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


Modulation of host responses by IFN-stimulated genes / response to alcohol / FK506 binding / MECP2 regulates neuronal receptors and channels / : / heat shock protein binding / ESR-mediated signaling / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / response to cocaine / peptidylprolyl isomerase ...Modulation of host responses by IFN-stimulated genes / response to alcohol / FK506 binding / MECP2 regulates neuronal receptors and channels / : / heat shock protein binding / ESR-mediated signaling / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / response to cocaine / peptidylprolyl isomerase / response to bacterium / peptidyl-prolyl cis-trans isomerase activity / protein folding / protein-macromolecule adaptor activity / extracellular exosome / nucleoplasm / membrane / cytoplasm / cytosol
Similarity search - Function
: / Chitinase A; domain 3 - #40 / Tetratricopeptide repeat / Chitinase A; domain 3 / Tetratricopeptide repeat / FKBP-type peptidyl-prolyl cis-trans isomerase / FKBP-type peptidyl-prolyl cis-trans isomerase domain / FKBP-type peptidyl-prolyl cis-trans isomerase domain profile. / TPR repeat region circular profile. / Peptidyl-prolyl cis-trans isomerase domain superfamily ...: / Chitinase A; domain 3 - #40 / Tetratricopeptide repeat / Chitinase A; domain 3 / Tetratricopeptide repeat / FKBP-type peptidyl-prolyl cis-trans isomerase / FKBP-type peptidyl-prolyl cis-trans isomerase domain / FKBP-type peptidyl-prolyl cis-trans isomerase domain profile. / TPR repeat region circular profile. / Peptidyl-prolyl cis-trans isomerase domain superfamily / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Chem-3JP / Peptidyl-prolyl cis-trans isomerase FKBP5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.08 Å
AuthorsPomplun, S. / Wang, Y. / Kirschner, K. / Kozany, C. / Bracher, A. / Hausch, F.
Citation
Journal: Angew.Chem.Int.Ed.Engl. / Year: 2015
Title: Rational Design and Asymmetric Synthesis of Potent and Neurotrophic Ligands for FK506-Binding Proteins (FKBPs).
Authors: Pomplun, S. / Wang, Y. / Kirschner, A. / Kozany, C. / Bracher, A. / Hausch, F.
#1: Journal: Acta Cryst. 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
DepositionAug 27, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 3, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 14, 2015Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5982
Polymers14,0261
Non-polymers5721
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)42.044, 54.638, 56.779
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Detailsbiological unit is a monomer

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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, UNP residues 16-140 / Mutation: yes
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) / Strain (production host): codon+ RIL / References: UniProt: Q13451, peptidylprolyl isomerase
#2: Chemical ChemComp-3JP / (1S,5S,6R)-10-[(3,5-dichlorophenyl)sulfonyl]-3-[2-(3,4-dimethoxyphenoxy)ethyl]-5-ethyl-3,10-diazabicyclo[4.3.1]decan-2-one


Mass: 571.513 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H32Cl2N2O6S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 218 / 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: 47.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 37 % PEG-3350, 8 % DMSO, 2 mM ligand, 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: SLS / Beamline: X10SA / Wavelength: 0.8 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 14, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 1.08→56.779 Å / Num. all: 53393 / Num. obs: 53393 / % possible obs: 94.2 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.037 / Rrim(I) all: 0.072 / Rsym value: 0.062 / Net I/av σ(I): 5.385 / Net I/σ(I): 10.5 / Num. measured all: 192898
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
1.08-1.143.80.352.22810974730.2040.353.291.5
1.14-1.213.70.25332666072980.150.2534.394.2
1.21-1.293.50.2033.82449569210.1220.2035.395.3
1.29-1.393.70.164.72298162640.0940.166.892.2
1.39-1.533.30.1265.81792554050.0780.126886.5
1.53-1.713.70.0838.52007754560.0490.08312.595.6
1.71-1.973.80.06110.21889350320.0360.06117.399.1
1.97-2.413.50.04912.31485342440.030.04921.898.4
2.41-3.413.70.04511.51236033620.0270.04525.299.3
3.41-56.7793.40.04212.2654519380.0270.04227.198.4

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Processing

Software
NameVersionClassificationNB
SCALA3.2.25data scaling
REFMAC5.2.0019refinement
PDB_EXTRACT3.15data extraction
XSCALEdata scaling
XDSdata reduction
XSCALEdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3O5Q

3o5q


Resolution: 1.08→20 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.969 / WRfactor Rfree: 0.181 / WRfactor Rwork: 0.1556 / FOM work R set: 0.9247 / SU B: 0.754 / SU ML: 0.017 / SU R Cruickshank DPI: 0.0306 / SU Rfree: 0.0302 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.031 / ESU R Free: 0.03 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1692 2617 4.9 %RANDOM
Rwork0.1509 50708 --
obs0.1518 50708 93.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 36.93 Å2 / Biso mean: 8.146 Å2 / Biso min: 5.24 Å2
Baniso -1Baniso -2Baniso -3
1--0.21 Å20 Å20 Å2
2--0.12 Å20 Å2
3---0.09 Å2
Refinement stepCycle: final / Resolution: 1.08→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms982 0 37 224 1243
Biso mean--13.75 19.85 -
Num. residues----128
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0221087
X-RAY DIFFRACTIONr_bond_other_d0.0080.02761
X-RAY DIFFRACTIONr_angle_refined_deg1.722.0231472
X-RAY DIFFRACTIONr_angle_other_deg0.8523.0041842
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9735137
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.5722540
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.44815197
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.392153
X-RAY DIFFRACTIONr_chiral_restr0.3310.2156
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021203
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02199
X-RAY DIFFRACTIONr_nbd_refined0.2050.2199
X-RAY DIFFRACTIONr_nbd_other0.1910.2811
X-RAY DIFFRACTIONr_nbtor_refined0.1810.2548
X-RAY DIFFRACTIONr_nbtor_other0.0950.2573
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1880.2150
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1690.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2390.228
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1430.238
X-RAY DIFFRACTIONr_mcbond_it1.4191.5713
X-RAY DIFFRACTIONr_mcbond_other0.5071.5275
X-RAY DIFFRACTIONr_mcangle_it1.81621083
X-RAY DIFFRACTIONr_scbond_it2.6763476
X-RAY DIFFRACTIONr_scangle_it3.3294.5389
X-RAY DIFFRACTIONr_rigid_bond_restr1.26432073
X-RAY DIFFRACTIONr_sphericity_free5.2163224
X-RAY DIFFRACTIONr_sphericity_bonded2.84231820
LS refinement shellResolution: 1.08→1.108 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.192 172 -
Rwork0.18 3583 -
all-3755 -
obs--90.94 %

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