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- PDB-8baj: Structure of the FK1 domain of the FKBP51 G64S variant in complex... -

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Basic information

Entry
Database: PDB / ID: 8baj
TitleStructure of the FK1 domain of the FKBP51 G64S variant 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 / Isomerase Inhibitor Complex
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 / response to bacterium ...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 / response to bacterium / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / protein folding / protein-macromolecule adaptor activity / extracellular exosome / nucleoplasm / membrane / cytoplasm / cytosol
Similarity search - Function
: / Tetratricopeptide repeat / 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 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
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: 1.2 Å
AuthorsMeyners, C. / Hausch, F.
Funding support Germany, 1items
OrganizationGrant numberCountry
Hessian Ministry of Science, Higher Education and Art (HMWK) Germany
CitationJournal: Front Mol Biosci / Year: 2022
Title: Binding pocket stabilization by high-throughput screening of yeast display libraries.
Authors: Lerma Romero, J.A. / Meyners, C. / Christmann, A. / Reinbold, L.M. / Charalampidou, A. / Hausch, F. / Kolmar, H.
History
DepositionOct 11, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 16, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 7, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jan 31, 2024Group: 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
A: Peptidyl-prolyl cis-trans isomerase FKBP5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5182
Polymers14,0341
Non-polymers4841
Water2,810156
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.856, 54.242, 56.864
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 / 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: 14034.053 Da / Num. of mol.: 1 / Mutation: A19T C103A C107I G64S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FKBP5, AIG6, FKBP51 / Production host: Escherichia coli BL21 (bacteria) / 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 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 156 / 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: 2.24 Å3/Da / Density % sol: 45.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 40% PEG3350 0.1M HEPES-NaOH pH 7.5 0.2M ammonium acetate

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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 18, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.2→40.86 Å / Num. obs: 39512 / % possible obs: 98.4 % / Redundancy: 6.8 % / CC1/2: 0.993 / Rmerge(I) obs: 0.115 / Rpim(I) all: 0.068 / Rrim(I) all: 0.134 / Net I/σ(I): 5.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
6.57-40.8660.1263040.9870.0710.145
1.2-1.226.81.36218590.5590.8241.597

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5OBK

5obk


Resolution: 1.2→39.28 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.954 / SU B: 2.064 / SU ML: 0.039 / Cross valid method: THROUGHOUT / ESU R: 0.044 / ESU R Free: 0.045
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2096 1941 4.918 %
Rwork0.1751 37523 -
all0.177 --
obs-39464 98.086 %
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: 13.269 Å2
Baniso -1Baniso -2Baniso -3
1-1.963 Å20 Å2-0 Å2
2---1.889 Å20 Å2
3----0.074 Å2
Refinement stepCycle: LAST / Resolution: 1.2→39.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms940 0 31 156 1127
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0121010
X-RAY DIFFRACTIONr_bond_other_d0.0020.016932
X-RAY DIFFRACTIONr_angle_refined_deg1.7131.691372
X-RAY DIFFRACTIONr_angle_other_deg0.5911.6152167
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2375130
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.63953
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.23810160
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.8991034
X-RAY DIFFRACTIONr_chiral_restr0.2860.2153
X-RAY DIFFRACTIONr_chiral_restr_other0.0360.26
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021135
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02198
X-RAY DIFFRACTIONr_nbd_refined0.2050.2163
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1880.2865
X-RAY DIFFRACTIONr_nbtor_refined0.1770.2517
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0840.2519
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1160.298
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2290.210
X-RAY DIFFRACTIONr_nbd_other0.1520.237
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1670.224
X-RAY DIFFRACTIONr_mcbond_it1.7811.287520
X-RAY DIFFRACTIONr_mcbond_other1.7821.287519
X-RAY DIFFRACTIONr_mcangle_it2.171.939650
X-RAY DIFFRACTIONr_mcangle_other2.1681.939651
X-RAY DIFFRACTIONr_scbond_it2.3921.557490
X-RAY DIFFRACTIONr_scbond_other2.3891.558491
X-RAY DIFFRACTIONr_scangle_it2.7692.212722
X-RAY DIFFRACTIONr_scangle_other2.7682.213723
X-RAY DIFFRACTIONr_lrange_it3.62627.7461178
X-RAY DIFFRACTIONr_lrange_other3.18321.871122
X-RAY DIFFRACTIONr_rigid_bond_restr4.65831942
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
1.2-1.2310.3281290.29626870.29729500.9340.95295.45760.295
1.231-1.2650.3081230.27426040.27628370.9380.95796.12270.273
1.265-1.3020.2751530.25725480.25827810.9450.96397.12330.253
1.302-1.3420.2731390.24424790.24526950.9470.96697.14290.237
1.342-1.3850.2471280.20624380.20826350.9570.97797.38140.197
1.385-1.4340.221160.18523710.18725310.9760.98198.26160.175
1.434-1.4880.2021370.15922810.16124650.9770.98798.09330.147
1.488-1.5490.2151120.15822000.1623660.9730.98797.71770.145
1.549-1.6180.2261020.1421280.14322610.9730.98998.62890.13
1.618-1.6960.1841150.13220390.13521840.980.99198.62640.124
1.696-1.7880.182730.13419760.13620750.9790.9998.7470.13
1.788-1.8960.177720.11818770.1219630.9840.99299.28680.119
1.896-2.0270.1851120.12517220.12818540.9830.99198.92120.132
2.027-2.1890.175880.12916520.13117500.9830.9999.42860.138
2.189-2.3970.161020.14314840.14515930.9830.98799.56060.163
2.397-2.6780.255550.17113970.17314550.9550.98399.79380.203
2.678-3.090.196700.17912200.1812940.9740.9899.69090.223
3.09-3.7790.222580.19710680.19811270.9720.97899.91130.249
3.779-5.320.191350.1798420.1798770.9740.9811000.231
5.32-39.280.245220.2595100.2595410.9510.95398.33640.367

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