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- PDB-7a6x: Structure of the FKBP51FK1 domain in complex with the macrocyclic... -

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Basic information

Entry
Database: PDB / ID: 7a6x
TitleStructure of the FKBP51FK1 domain in complex with the macrocyclic SAFit analogue 56
ComponentsPeptidyl-prolyl cis-trans isomerase FKBP5
KeywordsISOMERASE / Inhibitor / Complex / SAFit / FKBP
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-R3B / Peptidyl-prolyl cis-trans isomerase FKBP5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.67 Å
AuthorsBauder, M. / Meyners, C. / Purder, P. / Merz, S. / Voll, A. / Heymann, T. / Hausch, F.
CitationJournal: J.Med.Chem. / Year: 2021
Title: Structure-Based Design of High-Affinity Macrocyclic FKBP51 Inhibitors.
Authors: Bauder, M. / Meyners, C. / Purder, P.L. / Merz, S. / Sugiarto, W.O. / Voll, A.M. / Heymann, T. / Hausch, F.
History
DepositionAug 27, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 17, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 7, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jan 31, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)14,9892
Polymers14,2731
Non-polymers7161
Water90150
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.565, 47.821, 61.468
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: 14273.369 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 (bacteria) / References: UniProt: Q13451, peptidylprolyl isomerase
#2: Chemical ChemComp-R3B / (2S,9S,12R)-2-cyclohexyl-12-[2-(3,4-dimethoxyphenyl)ethyl]-24,27-dimethoxy-11,18,22-trioxa-4-azatetracyclo[21.2.2.113,17.04,9]octacosa-1(25),13(28),14,16,23,26-hexaene-3,10-dione


Mass: 715.872 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C42H53NO9 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / 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: 1.78 Å3/Da / Density % sol: 30.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 30% PEG-3350, 0.2 M NH4-acetate and 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 PILATUS 6M / Detector: PIXEL / Date: Jun 6, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.4→30.73 Å / Num. obs: 19573 / % possible obs: 95 % / Redundancy: 6.2 % / CC1/2: 0.996 / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.046 / Rrim(I) all: 0.087 / Net I/σ(I): 10.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
7.54-30.735.70.0331680.9980.020.03997.8
1.4-1.426.31.0619890.6420.6751.26196.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
REFMAC5.8.0258refinement
DIALSdata collection
Aimless0.7.4data reduction
Aimless0.7.4data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4TW7

4tw7


Resolution: 1.67→20.001 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.953 / SU B: 4.274 / SU ML: 0.065 / Cross valid method: THROUGHOUT / ESU R: 0.179 / ESU R Free: 0.103
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1985 565 4.837 %
Rwork0.1505 11116 -
all0.153 --
obs-11681 94.537 %
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: 17.831 Å2
Baniso -1Baniso -2Baniso -3
1-0.746 Å2-0 Å20 Å2
2--0.174 Å2-0 Å2
3----0.92 Å2
Refinement stepCycle: LAST / Resolution: 1.67→20.001 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms890 0 52 50 992
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.013974
X-RAY DIFFRACTIONr_bond_other_d0.0050.018934
X-RAY DIFFRACTIONr_angle_refined_deg1.5941.7151314
X-RAY DIFFRACTIONr_angle_other_deg1.5091.6912166
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4545119
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.87122.77836
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.40815160
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.751153
X-RAY DIFFRACTIONr_chiral_restr0.0540.2122
X-RAY DIFFRACTIONr_chiral_restr_other1.2080.218
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021059
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02196
X-RAY DIFFRACTIONr_nbd_refined0.1940.2166
X-RAY DIFFRACTIONr_symmetry_nbd_other0.180.2843
X-RAY DIFFRACTIONr_nbtor_refined0.1670.2475
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0750.2446
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.130.239
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2560.211
X-RAY DIFFRACTIONr_nbd_other0.2580.257
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1150.213
X-RAY DIFFRACTIONr_mcbond_it1.6871.721479
X-RAY DIFFRACTIONr_mcbond_other1.6881.721478
X-RAY DIFFRACTIONr_mcangle_it2.2852.589597
X-RAY DIFFRACTIONr_mcangle_other2.2832.588598
X-RAY DIFFRACTIONr_scbond_it1.7241.971495
X-RAY DIFFRACTIONr_scbond_other1.7231.971496
X-RAY DIFFRACTIONr_scangle_it2.1982.82717
X-RAY DIFFRACTIONr_scangle_other2.1962.821718
X-RAY DIFFRACTIONr_lrange_it2.98120.6581058
X-RAY DIFFRACTIONr_lrange_other2.9520.6081055
X-RAY DIFFRACTIONr_rigid_bond_restr0.94531908
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
1.67-1.7130.27440.1258100.1328920.9240.96495.73990.113
1.713-1.760.24410.1457770.1498540.9160.94995.78450.13
1.76-1.810.189400.1527620.1548550.9440.94293.80120.134
1.81-1.8650.256360.1526460.1588050.920.94384.72050.135
1.865-1.9260.235370.1237460.1288150.9290.96296.07360.109
1.926-1.9930.227330.1147040.1187630.940.97396.59240.106
1.993-2.0670.164340.1286860.137450.9630.96996.64430.12
2.067-2.1510.23300.1426800.1457230.9450.96298.20190.132
2.151-2.2450.217270.1436280.1466820.9290.9696.04110.137
2.245-2.3540.219370.1595610.1636730.940.94788.85590.15
2.354-2.4790.291320.1485840.1556450.9260.96195.50390.146
2.479-2.6270.198200.1515570.1525900.9510.96297.79660.149
2.627-2.8050.226170.1635510.1655840.9530.9697.26030.162
2.805-3.0240.17190.1614870.1625200.9510.96497.30770.165
3.024-3.3060.153280.1594360.1584950.9720.96893.73740.164
3.306-3.6830.167260.1443790.1464620.970.97587.66230.154
3.683-4.2290.173250.1313740.1344050.9750.9898.51850.145
4.229-5.1230.154200.1433260.1443530.9760.97998.0170.167
5.123-7.0180.267100.2122400.2142900.9530.95886.20690.233
7.018-20.0010.17290.231770.2271890.9640.95398.41270.256

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