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- PDB-7b9y: Structure of the FKBP51FK1 domain in complex with the macrocyclic... -

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Basic information

Entry
Database: PDB / ID: 7b9y
TitleStructure of the FKBP51FK1 domain in complex with the macrocyclic SAFit analogue 64a
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-T5B / Peptidyl-prolyl cis-trans isomerase FKBP5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsBauder, M. / Meyners, C. / Purder, P. / Merz, S. / Voll, A. / Heymann, T. / Hausch, F.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)HA5565-5/1 Germany
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
DepositionDec 15, 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
A: Peptidyl-prolyl cis-trans isomerase FKBP5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,0352
Polymers14,2731
Non-polymers7621
Water2,756153
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.510, 48.510, 105.935
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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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(DE3) (bacteria) / References: UniProt: Q13451, peptidylprolyl isomerase
#2: Chemical ChemComp-T5B / 2-cyclohexyl-12-[2-(3,4-dimethoxyphenyl)ethyl]-20,21-dihydroxy-25,26-dimethoxy-11,18,23-trioxa-4-azatetracyclo[22.3.1.113,17.04,9]nonacosa-1(27),13(29),14,16,24(28),25-hexaene-3,10-dione


Mass: 761.897 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C43H55NO11 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 153 / 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: 2.52 Å3/Da / Density % sol: 51.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 18% PEG 3350, 0.1 M HEPES pH 7.5, 0.2M ammonium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.97626 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 26, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97626 Å / Relative weight: 1
ReflectionResolution: 1.35→105.93 Å / Num. obs: 32570 / % possible obs: 100 % / Redundancy: 19.1 % / CC1/2: 1 / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.02 / Rrim(I) all: 0.065 / Net I/σ(I): 21.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
7.39-105.9315.80.0432590.9990.0140.045
1.35-1.3716.11.49915850.7740.5491.598

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
REFMAC5.8.0267refinement
XDSdata collection
Aimless0.7.4data reduction
Aimless0.7.4data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4tw7

4tw7


Resolution: 1.35→39.003 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.976 / WRfactor Rfree: 0.166 / WRfactor Rwork: 0.139 / SU B: 1.45 / SU ML: 0.027 / Average fsc free: 0.9671 / Average fsc work: 0.9723 / Cross valid method: THROUGHOUT / ESU R: 0.048 / ESU R Free: 0.044
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1583 1623 4.992 %
Rwork0.1353 30892 -
all0.137 --
obs-32515 99.948 %
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: 22.85 Å2
Baniso -1Baniso -2Baniso -3
1-0.188 Å20.094 Å20 Å2
2--0.188 Å2-0 Å2
3----0.61 Å2
Refinement stepCycle: LAST / Resolution: 1.35→39.003 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms969 0 55 153 1177
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0131163
X-RAY DIFFRACTIONr_bond_other_d0.0060.0181122
X-RAY DIFFRACTIONr_angle_refined_deg2.3061.7081585
X-RAY DIFFRACTIONr_angle_other_deg1.8551.6782614
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.935151
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.23124.09144
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.98415201
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.746153
X-RAY DIFFRACTIONr_chiral_restr0.1310.2148
X-RAY DIFFRACTIONr_chiral_restr_other1.5470.217
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.021337
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02244
X-RAY DIFFRACTIONr_nbd_refined0.2260.2224
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1910.2989
X-RAY DIFFRACTIONr_nbtor_refined0.1820.2536
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0930.2511
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2010.2105
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1930.23
X-RAY DIFFRACTIONr_nbd_other0.1290.243
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1560.212
X-RAY DIFFRACTIONr_mcbond_it3.4512.12577
X-RAY DIFFRACTIONr_mcbond_other3.4512.12577
X-RAY DIFFRACTIONr_mcangle_it4.4083.174737
X-RAY DIFFRACTIONr_mcangle_other4.4053.173738
X-RAY DIFFRACTIONr_scbond_it4.4142.429586
X-RAY DIFFRACTIONr_scbond_other4.412.428587
X-RAY DIFFRACTIONr_scangle_it5.1983.488848
X-RAY DIFFRACTIONr_scangle_other5.1963.487849
X-RAY DIFFRACTIONr_lrange_it5.48826.7481317
X-RAY DIFFRACTIONr_lrange_other5.41825.9261279
X-RAY DIFFRACTIONr_rigid_bond_restr4.86532283
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
1.35-1.3850.1961220.21122440.21123770.9440.93699.53720.207
1.385-1.4230.181970.17222310.17223280.9430.9551000.162
1.423-1.4640.1881080.1520920.15222000.9550.9621000.137
1.464-1.5090.1871370.13720490.1421860.9580.9661000.123
1.509-1.5590.1671020.1120300.11321320.9670.9761000.099
1.559-1.6130.141050.10619480.10820530.9720.9791000.093
1.613-1.6740.165750.10218930.10419680.9670.9781000.091
1.674-1.7420.134890.10518110.10719000.9790.9791000.095
1.742-1.820.144770.10517480.10718250.9760.9821000.097
1.82-1.9080.149840.10916870.11117710.9770.9791000.103
1.908-2.0110.145820.1115990.11216810.9790.9831000.107
2.011-2.1330.133790.10915070.1115860.9810.9851000.107
2.133-2.280.156770.11414340.11615110.9750.9821000.115
2.28-2.4610.15630.11613360.11713990.9730.9811000.118
2.461-2.6950.159810.12312220.12513030.9720.9791000.131
2.695-3.0120.156680.13311170.13511850.9720.9751000.145
3.012-3.4740.194680.1549860.15710550.9630.97499.90520.174
3.474-4.2470.155600.1418370.1428980.9810.98199.88860.169
4.247-5.970.095320.1576960.1547280.9890.9831000.199
5.97-39.0030.301170.2354250.2374430.9470.95899.77430.285

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