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- PDB-8ba6: Structure of the FK1 domain of the FKBP51 G64S variant in complex... -

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Basic information

Entry
Database: PDB / ID: 8ba6
TitleStructure of the FK1 domain of the FKBP51 G64S variant in complex with (2R,5S,12R)-12-cyclohexyl-2-[2-(3,4-dimethoxyphenyl)ethyl]-15,15,16-trimethyl-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
KeywordsISOMERASE / Isomerase Inhibitor Complex
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 / 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-S8N / Peptidyl-prolyl cis-trans isomerase FKBP5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 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

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)14,7122
Polymers14,0341
Non-polymers6781
Water3,981221
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.575, 50.420, 59.073
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-S8N / (2~{R},5~{S},12~{R})-12-cyclohexyl-2-[2-(3,4-dimethoxyphenyl)ethyl]-15,15,16-trimethyl-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: 677.827 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C38H51N3O8 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 221 / 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: 46.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 30% PEG3350 0.2M ammonium acetate 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: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 18, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.1→38.35 Å / Num. obs: 50803 / % possible obs: 95.2 % / Redundancy: 6.6 % / CC1/2: 1 / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.032 / Rrim(I) all: 0.061 / Net I/σ(I): 16.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
6.02-38.355.90.0183860.9990.0110.021
1.1-1.126.70.78123400.7450.4830.92

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
XDSdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7AWF

7awf


Resolution: 1.1→29.554 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.975 / SU B: 1.376 / SU ML: 0.028 / Cross valid method: THROUGHOUT / ESU R: 0.03 / ESU R Free: 0.03
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1604 2537 4.998 %
Rwork0.1397 48219 -
all0.141 --
obs-50756 94.784 %
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: 12.06 Å2
Baniso -1Baniso -2Baniso -3
1--2.398 Å2-0 Å20 Å2
2--1.71 Å2-0 Å2
3---0.688 Å2
Refinement stepCycle: LAST / Resolution: 1.1→29.554 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms975 0 49 221 1245
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0121130
X-RAY DIFFRACTIONr_bond_other_d0.0050.0171064
X-RAY DIFFRACTIONr_angle_refined_deg1.771.7081538
X-RAY DIFFRACTIONr_angle_other_deg1.0131.6622497
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9555145
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.35352
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.98410197
X-RAY DIFFRACTIONr_dihedral_angle_6_deg17.3511041
X-RAY DIFFRACTIONr_chiral_restr0.1080.2162
X-RAY DIFFRACTIONr_chiral_restr_other1.1810.217
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.021285
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02213
X-RAY DIFFRACTIONr_nbd_refined0.2630.2179
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1860.2950
X-RAY DIFFRACTIONr_nbtor_refined0.180.2559
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0840.2564
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2010.2135
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2590.24
X-RAY DIFFRACTIONr_nbd_other0.2040.236
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1680.231
X-RAY DIFFRACTIONr_mcbond_it3.2761.139559
X-RAY DIFFRACTIONr_mcbond_other3.2761.139559
X-RAY DIFFRACTIONr_mcangle_it3.5631.691711
X-RAY DIFFRACTIONr_mcangle_other3.5611.691712
X-RAY DIFFRACTIONr_scbond_it4.2211.366571
X-RAY DIFFRACTIONr_scbond_other4.2171.365572
X-RAY DIFFRACTIONr_scangle_it4.2481.932827
X-RAY DIFFRACTIONr_scangle_other4.2451.932828
X-RAY DIFFRACTIONr_lrange_it5.50328.4381342
X-RAY DIFFRACTIONr_lrange_other4.56123.7791272
X-RAY DIFFRACTIONr_rigid_bond_restr14.33332194
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
1.1-1.1290.2351730.20933390.2139100.9590.97689.8210.199
1.129-1.1590.2011550.18633450.18738060.970.98191.96010.172
1.159-1.1930.171690.16432520.16436970.9850.98692.53450.148
1.193-1.230.1851640.17831610.17836130.9770.9892.02880.16
1.23-1.270.1741610.15631230.15734940.9850.98793.98970.138
1.27-1.3140.1591570.14330270.14433790.980.98994.22910.125
1.314-1.3640.1761350.1429720.14132730.9770.98994.92820.121
1.364-1.4190.1641610.13128340.13331270.9830.9995.77870.115
1.419-1.4820.1671300.12927440.13130350.9820.98994.69520.112
1.482-1.5550.1391320.10326440.10529010.9870.99495.69110.089
1.555-1.6380.1461280.10425450.10627520.9890.99497.12940.091
1.638-1.7370.1531460.11424050.11726350.9860.99296.81210.102
1.737-1.8570.1551070.11322980.11524530.9830.99298.04320.103
1.857-2.0050.1511150.1221180.12223040.9870.99296.91840.112
2.005-2.1950.1481170.12619150.12721370.9890.99195.08660.12
2.195-2.4530.1691320.12617750.12919410.9830.9998.24830.122
2.453-2.8290.135850.13916120.13917210.9870.98798.60550.137
2.829-3.4570.168790.15213750.15314820.9810.98698.11070.158
3.457-4.8560.127570.13810710.13811810.9920.98995.51230.151
4.856-29.5540.241340.216640.2117050.9610.97599.00710.225

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