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- PDB-8ccg: The Fk1 domain of FKBP51 in complex with (2R,5S,12S)-12-(thiophen... -

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Basic information

Entry
Database: PDB / ID: 8ccg
TitleThe Fk1 domain of FKBP51 in complex with (2R,5S,12S)-12-(thiophen-2-yl)-2-[2-(3,4-dimethoxyphenyl)ethyl]-15,15-dimethyl-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 / FKBP51 / SAFit / Inhibitor
Function / homology
Function and homology information


FK506 binding / MECP2 regulates neuronal receptors and channels / chaperone-mediated protein folding / 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 / MECP2 regulates neuronal receptors and channels / chaperone-mediated protein folding / 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 / cytosol / cytoplasm
Similarity search - Function
: / Tetratricopeptide repeat / 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 / 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-UBK / Peptidyl-prolyl cis-trans isomerase FKBP5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsMeyners, C. / Knaup, F.H. / Walz, C.M. / Hausch, F.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Federal Ministry for Education and Research Germany
CitationJournal: J.Med.Chem. / Year: 2023
Title: Structure-Based Discovery of a New Selectivity-Enabling Motif for the FK506-Binding Protein 51.
Authors: Knaup, F.H. / Meyners, C. / Sugiarto, W.O. / Wedel, S. / Springer, M. / Walz, C. / Geiger, T.M. / Schmidt, M. / Sisignano, M. / Hausch, F.
History
DepositionJan 27, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 26, 2023Provider: repository / Type: Initial release
Revision 1.1May 10, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)14,6682
Polymers14,0041
Non-polymers6641
Water2,882160
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.821, 48.073, 58.549
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-UBK / (2~{R},5~{S},12~{S})-2-[2-(3,4-dimethoxyphenyl)ethyl]-15,15-dimethyl-12-thiophen-2-yl-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: 663.780 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C35H41N3O8S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 160 / 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: 2.4 Å3/Da / Density % sol: 48.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 32% PEG3350, 0.1 M HEPES pH 7.5, 0.2 M 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 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: 1.3→48.07 Å / Num. obs: 33862 / % possible obs: 99.9 % / Redundancy: 6.3 % / CC1/2: 1 / Rmerge(I) obs: 0.034 / Rpim(I) all: 0.022 / Rrim(I) all: 0.041 / Net I/σ(I): 18
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
7.12-48.075.50.01425810.0090.017
1.3-1.326.51.51916160.6780.9551.801

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Processing

Software
NameVersionClassification
REFMAC5.8.0403refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4TW7

4tw7


Resolution: 1.3→33.926 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.965 / SU B: 2.992 / SU ML: 0.053 / Cross valid method: THROUGHOUT / ESU R: 0.051 / ESU R Free: 0.05
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1998 1751 5.18 %
Rwork0.1665 32055 -
all0.168 --
obs-33806 99.82 %
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: 19.858 Å2
Baniso -1Baniso -2Baniso -3
1--2.484 Å2-0 Å20 Å2
2--0.122 Å2-0 Å2
3---2.362 Å2
Refinement stepCycle: LAST / Resolution: 1.3→33.926 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms942 0 47 160 1149
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0121023
X-RAY DIFFRACTIONr_bond_other_d0.0030.016959
X-RAY DIFFRACTIONr_angle_refined_deg1.8771.7111387
X-RAY DIFFRACTIONr_angle_other_deg0.7091.6432212
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.0055128
X-RAY DIFFRACTIONr_dihedral_angle_2_deg4.26552
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.72410151
X-RAY DIFFRACTIONr_dihedral_angle_6_deg18.6211036
X-RAY DIFFRACTIONr_chiral_restr0.0850.2150
X-RAY DIFFRACTIONr_chiral_restr_other1.0230.211
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021163
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02216
X-RAY DIFFRACTIONr_nbd_refined0.2220.2164
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1910.2895
X-RAY DIFFRACTIONr_nbtor_refined0.1750.2519
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0870.2492
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1340.289
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1080.23
X-RAY DIFFRACTIONr_nbd_other0.1630.225
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1260.217
X-RAY DIFFRACTIONr_mcbond_it1.8922.185515
X-RAY DIFFRACTIONr_mcbond_other1.8912.185515
X-RAY DIFFRACTIONr_mcangle_it2.3553.947642
X-RAY DIFFRACTIONr_mcangle_other2.3543.945643
X-RAY DIFFRACTIONr_scbond_it1.9122.322508
X-RAY DIFFRACTIONr_scbond_other1.912.321509
X-RAY DIFFRACTIONr_scangle_it2.5414.181745
X-RAY DIFFRACTIONr_scangle_other2.544.179746
X-RAY DIFFRACTIONr_lrange_it3.51925.9881156
X-RAY DIFFRACTIONr_lrange_other3.23422.731113
X-RAY DIFFRACTIONr_rigid_bond_restr4.23331982
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
1.3-1.3340.2951300.28923250.28924600.9710.97399.79670.284
1.334-1.370.2641270.26622590.26623900.9780.97799.83260.253
1.37-1.410.2721090.24722230.24823350.9610.97799.87150.229
1.41-1.4530.2571370.21421390.21722790.9690.98399.86840.191
1.453-1.5010.2691180.19520790.19921990.9730.98599.9090.168
1.501-1.5530.2171310.16719970.1721310.970.9999.85920.139
1.553-1.6120.1931110.14519670.14820790.9860.99199.95190.12
1.612-1.6770.2271020.14218650.14619710.9740.99199.79710.12
1.677-1.7520.198810.13718390.1419200.980.9911000.117
1.752-1.8370.179960.1317390.13318380.9860.99299.83680.113
1.837-1.9360.1981070.12816460.13217540.9770.99199.9430.116
1.936-2.0530.181670.15515860.15716540.9670.98599.93950.144
2.053-2.1940.194470.14515040.14615560.9740.98999.67870.141
2.194-2.3690.174990.13513670.13714690.9810.9999.79580.13
2.369-2.5940.167680.14812750.14913440.9830.98699.92560.149
2.594-2.8980.18780.16511590.16612420.9750.98299.59740.17
2.898-3.3430.218460.16710290.16910820.9610.98399.35310.178
3.343-4.0840.233430.1719100.1749530.9640.9831000.191
4.084-5.7340.16340.1637110.1637470.9850.98699.73230.194
5.734-33.9260.23200.2434360.2424620.9680.96598.70130.282

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