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- PDB-8ccc: The Fk1 domain of FKBP51 in complex with 2-(3-((R)-1-(((S)-1-((S)... -

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Basic information

Entry
Database: PDB / ID: 8ccc
TitleThe Fk1 domain of FKBP51 in complex with 2-(3-((R)-1-(((S)-1-((S)-2-(5-chlorothiophen-2-yl)propanoyl)piperidine-2-carbonyl)oxy)-3-(3,4-dimethoxyphenyl)propyl)phenoxy)acetic acid
ComponentsPeptidyl-prolyl cis-trans isomerase FKBP5
KeywordsISOMERASE / FKBP51 / SAFit / Inhibitor
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 / extracellular exosome / nucleoplasm / membrane / cytosol / cytoplasm
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-UCT / Peptidyl-prolyl cis-trans isomerase FKBP5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 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

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Assembly

Deposited unit
A: Peptidyl-prolyl cis-trans isomerase FKBP5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6342
Polymers14,0041
Non-polymers6301
Water1,51384
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.651, 50.882, 58.103
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-UCT / 2-[3-[(1~{R})-1-[(2~{S})-1-[(2~{S})-2-(5-chloranylthiophen-2-yl)propanoyl]piperidin-2-yl]carbonyloxy-3-(3,4-dimethoxyphenyl)propyl]phenoxy]ethanoic acid


Mass: 630.148 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C32H36ClNO8S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 84 / 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: 2.57 Å3/Da / Density % sol: 52.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 22% 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: Sep 21, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.55→48.65 Å / Num. obs: 21573 / % possible obs: 99.9 % / Redundancy: 10.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.024 / Rrim(I) all: 0.059 / Net I/σ(I): 18.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
8.49-48.659.10.0331610.9980.0150.037
1.55-1.58101.21810560.8090.5811.353

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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: 1.55→38.308 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.948 / SU B: 8.26 / SU ML: 0.126 / Cross valid method: THROUGHOUT / ESU R: 0.088 / ESU R Free: 0.086
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2389 1064 4.969 %
Rwork0.2161 20348 -
all0.217 --
obs-21412 99.364 %
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: 32.336 Å2
Baniso -1Baniso -2Baniso -3
1--1.935 Å20 Å20 Å2
2--5.595 Å2-0 Å2
3----3.66 Å2
Refinement stepCycle: LAST / Resolution: 1.55→38.308 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms939 0 43 84 1066
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0121005
X-RAY DIFFRACTIONr_bond_other_d0.0030.016935
X-RAY DIFFRACTIONr_angle_refined_deg1.7271.7031362
X-RAY DIFFRACTIONr_angle_other_deg0.5931.6392155
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.5455127
X-RAY DIFFRACTIONr_dihedral_angle_2_deg4.20252
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.47510152
X-RAY DIFFRACTIONr_dihedral_angle_6_deg17.0621034
X-RAY DIFFRACTIONr_chiral_restr0.0680.2149
X-RAY DIFFRACTIONr_chiral_restr_other0.7610.210
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021143
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02208
X-RAY DIFFRACTIONr_nbd_refined0.2060.2184
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1890.2833
X-RAY DIFFRACTIONr_nbtor_refined0.1730.2512
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.2502
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1360.254
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0820.21
X-RAY DIFFRACTIONr_nbd_other0.1460.221
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0310.23
X-RAY DIFFRACTIONr_mcbond_it1.6782.066514
X-RAY DIFFRACTIONr_mcbond_other1.6782.066514
X-RAY DIFFRACTIONr_mcangle_it2.5273.712639
X-RAY DIFFRACTIONr_mcangle_other2.5253.711640
X-RAY DIFFRACTIONr_scbond_it2.1962.226491
X-RAY DIFFRACTIONr_scbond_other2.1942.227492
X-RAY DIFFRACTIONr_scangle_it3.4923.995723
X-RAY DIFFRACTIONr_scangle_other3.4913.996724
X-RAY DIFFRACTIONr_lrange_it6.03620.6961120
X-RAY DIFFRACTIONr_lrange_other5.98720.4151105
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
1.55-1.590.383730.35414770.35515510.7740.77599.93550.322
1.59-1.6340.341720.33414710.33415440.7790.77899.93520.3
1.634-1.6810.354680.3114160.31214840.7950.821000.276
1.681-1.7330.254710.29613430.29414150.8970.83799.92930.26
1.733-1.7890.275530.313550.29914080.9330.8631000.26
1.789-1.8520.272690.25513010.25613700.9020.9141000.229
1.852-1.9220.266650.30712090.30512990.8320.85198.07540.269
1.922-20.372630.30211790.30512750.8670.87397.41180.268
2-2.0890.257570.21811540.2212120.9640.96399.91750.203
2.089-2.190.206480.20511050.20511530.9620.9691000.194
2.19-2.3080.277500.24510360.24611350.9150.94695.68280.224
2.308-2.4480.173430.1759970.17510430.9730.97999.71240.172
2.448-2.6160.221630.1749350.1779980.9760.9811000.174
2.616-2.8250.246620.2118720.2139340.9590.9721000.213
2.825-3.0920.206480.2068040.2068520.9650.9731000.215
3.092-3.4550.24360.2157460.2167850.9650.97499.61780.23
3.455-3.9840.266530.1996400.2047040.9630.97798.43750.223
3.984-4.8660.193250.1545810.1566080.970.98599.67110.19
4.866-6.8260.187340.1914400.1914760.980.98299.57980.233
6.826-38.3080.227110.2322870.2323030.9840.96198.34980.283
Refinement TLS params.Method: refined / Origin x: 10.1509 Å / Origin y: 6.5202 Å / Origin z: 0.7216 Å
111213212223313233
T0.0356 Å2-0.009 Å20.0049 Å2-0.0194 Å2-0.0136 Å2--0.1095 Å2
L3.92 °2-0.1783 °20.7556 °2-3.4312 °20.6885 °2--3.9468 °2
S-0.0381 Å °-0.1599 Å °0.1277 Å °0.1435 Å °-0.0639 Å °0.1813 Å °0.1006 Å °-0.2452 Å °0.102 Å °
Refinement TLS groupSelection: ALL

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