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- PDB-8chp: The FK1 domain of FKBP51 in complex with (1S,5S,6R)-10-((S)-(3,5-... -

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Basic information

Entry
Database: PDB / ID: 8chp
TitleThe FK1 domain of FKBP51 in complex with (1S,5S,6R)-10-((S)-(3,5-dichlorophenyl)sulfinyl)-3-(pyridin-2-ylmethyl)-5-vinyl-3,10-diazabicyclo[4.3.1]decan-2-one
ComponentsPeptidyl-prolyl cis-trans isomerase FKBP5
KeywordsISOMERASE / FKBP51 / Inhibitor
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-UT6 / Peptidyl-prolyl cis-trans isomerase FKBP5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1 Å
AuthorsMeyners, C. / Purder, P.L. / Hausch, F.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Federal Ministry for Education and Research Germany
CitationJournal: Jacs Au / Year: 2023
Title: Deconstructing Protein Binding of Sulfonamides and Sulfonamide Analogues.
Authors: Purder, P.L. / Meyners, C. / Sugiarto, W.O. / Kolos, J. / Lohr, F. / Gebel, J. / Nehls, T. / Dotsch, V. / Lermyte, F. / Hausch, F.
History
DepositionFeb 8, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 6, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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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)14,4682
Polymers14,0041
Non-polymers4641
Water3,711206
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.306, 54.452, 56.405
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: 14004.026 Da / Num. of mol.: 1 / Mutation: A19T, C103A, C107I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FKBP5, AIG6, FKBP51 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q13451, peptidylprolyl isomerase
#2: Chemical ChemComp-UT6 / (1~{S},5~{S},6~{R})-10-[3,5-bis(chloranyl)phenyl]sulfinyl-5-ethenyl-3-(pyridin-2-ylmethyl)-3,10-diazabicyclo[4.3.1]decan-2-one


Mass: 464.408 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H23Cl2N3O2S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 206 / 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: 2.32 Å3/Da / Density % sol: 46.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 32% PEG3350, 0.2 M ammonium acetate, 0.1M HEPES-NaOH pH 7.5

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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: Sep 10, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1→42.31 Å / Num. obs: 71074 / % possible obs: 100 % / Redundancy: 7 % / CC1/2: 1 / Rmerge(I) obs: 0.031 / Rpim(I) all: 0.019 / Rrim(I) all: 0.037 / Net I/σ(I): 26.3
Reflection shell

Diffraction-ID: 1 / Redundancy: 6.8 %

Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
5.48-42.310.0235150.9990.0130.026
1-1.020.36334750.9230.2260.43

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Processing

Software
NameVersionClassification
REFMAC5.8.0403refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1→28.761 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.963 / SU B: 0.598 / SU ML: 0.016 / Cross valid method: THROUGHOUT / ESU R: 0.025 / ESU R Free: 0.026
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1871 3442 4.848 %
Rwork0.1751 67558 -
all0.176 --
obs-71000 99.931 %
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: 9.241 Å2
Baniso -1Baniso -2Baniso -3
1-0.012 Å20 Å20 Å2
2--0.091 Å2-0 Å2
3----0.103 Å2
Refinement stepCycle: LAST / Resolution: 1→28.761 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms961 0 30 206 1197
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0121044
X-RAY DIFFRACTIONr_bond_other_d0.0040.016968
X-RAY DIFFRACTIONr_angle_refined_deg1.9031.6841420
X-RAY DIFFRACTIONr_angle_other_deg0.8691.6112243
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4955135
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.68153
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.40310162
X-RAY DIFFRACTIONr_dihedral_angle_6_deg17.6311039
X-RAY DIFFRACTIONr_chiral_restr0.1340.2155
X-RAY DIFFRACTIONr_chiral_restr_other2.1450.25
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021215
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02224
X-RAY DIFFRACTIONr_nbd_refined0.2010.2182
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1980.2902
X-RAY DIFFRACTIONr_nbtor_refined0.1840.2519
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0840.2537
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.230.2121
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1450.26
X-RAY DIFFRACTIONr_nbd_other0.1650.235
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2350.238
X-RAY DIFFRACTIONr_mcbond_it0.9120.592534
X-RAY DIFFRACTIONr_mcbond_other0.910.591533
X-RAY DIFFRACTIONr_mcangle_it1.311.071671
X-RAY DIFFRACTIONr_mcangle_other1.3091.071672
X-RAY DIFFRACTIONr_scbond_it1.6320.813510
X-RAY DIFFRACTIONr_scbond_other1.6310.814511
X-RAY DIFFRACTIONr_scangle_it2.4721.411749
X-RAY DIFFRACTIONr_scangle_other2.471.412750
X-RAY DIFFRACTIONr_lrange_it5.18312.4841242
X-RAY DIFFRACTIONr_lrange_other4.8458.6741153
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
1-1.0260.2252420.22549390.22551820.9730.97199.98070.2
1.026-1.0540.212510.19247890.19350410.9730.97899.98020.17
1.054-1.0850.22340.18447060.18449480.9750.97999.83830.165
1.085-1.1180.2052090.17445720.17547840.9730.98199.93730.156
1.118-1.1540.1712120.16744260.16746420.9810.98299.91380.152
1.154-1.1950.1892350.16942330.1744690.9780.98299.97760.153
1.195-1.240.2032260.17541310.17643570.9730.9811000.161
1.24-1.290.1881790.17139800.17141610.9770.98299.95190.158
1.29-1.3480.1731940.16238260.16240210.9820.98499.97510.151
1.348-1.4130.1821710.16336840.16338570.9790.98399.94810.154
1.413-1.490.1681760.16834740.16836500.9810.9831000.16
1.49-1.580.171730.15632940.15734700.9840.98599.91350.153
1.58-1.6880.1971340.15931410.16132790.9760.98499.8780.161
1.688-1.8230.1711800.16728940.16830750.980.98399.96750.172
1.823-1.9960.1591440.17126610.1728070.9840.98299.92870.184
1.996-2.2310.1811370.16624510.16625930.9820.98399.80720.186
2.231-2.5730.1871310.17421430.17522760.9780.98199.91210.205
2.573-3.1450.194910.18618650.18619580.9760.97899.89790.224
3.145-4.4220.185700.17214700.17215420.9790.98299.87030.219
4.422-28.7610.241530.2298790.2299340.9560.97299.78590.312
Refinement TLS params.Method: refined / Origin x: -8.8436 Å / Origin y: -12.2634 Å / Origin z: 9.7118 Å
111213212223313233
T0.0076 Å2-0.0007 Å2-0.0024 Å2-0.0156 Å20.0069 Å2--0.0052 Å2
L0.7771 °20.2212 °20.0784 °2-1.3267 °20.1234 °2--0.4181 °2
S0.0142 Å °-0.0763 Å °-0.0594 Å °0.0891 Å °0.0068 Å °-0.0203 Å °0.028 Å °-0.0523 Å °-0.021 Å °
Refinement TLS groupSelection: ALL

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