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- PDB-7a6w: Structure of the FKBP51FK1 domain in complex with the macrocyclic... -

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Basic information

Entry
Database: PDB / ID: 7a6w
TitleStructure of the FKBP51FK1 domain in complex with the macrocyclic SAFit analogue 33-(Z)
ComponentsPeptidyl-prolyl cis-trans isomerase FKBP5
KeywordsISOMERASE / Inhibitor / Complex / SAFit / FKBP
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-R3E / Peptidyl-prolyl cis-trans isomerase FKBP5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 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
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
BBB: Peptidyl-prolyl cis-trans isomerase FKBP5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0914
Polymers28,5472
Non-polymers1,5442
Water75742
1
AAA: Peptidyl-prolyl cis-trans isomerase FKBP5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,0452
Polymers14,2731
Non-polymers7721
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
BBB: Peptidyl-prolyl cis-trans isomerase FKBP5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,0452
Polymers14,2731
Non-polymers7721
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.797, 47.869, 61.981
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number4
Space group name H-MP1211

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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.: 2
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-R3E / (2S,9S,12R,20Z)-2-cyclohexyl-12-[2-(3,4-dimethoxyphenyl)ethyl]-28,31-dimethoxy-11,18,23,26-tetraoxa-4-azatetracyclo[25.2.2.113,17.04,9]dotriaconta-1(29),13(32),14,16,20,27,30-heptaene-3,10-dione


Mass: 771.935 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C45H57NO10 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 42 / 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: 1.96 Å3/Da / Density % sol: 37.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 24% PEG-3350, 0.2 M NH4-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 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
Reflection twin
TypeCrystal-IDIDOperatorDomain-IDFraction
pseudo-merohedral11H, K, L10.5238
pseudo-merohedral22-h,-k,l20.4762
ReflectionResolution: 1.5→32.27 Å / Num. obs: 34142 / % possible obs: 96.1 % / Redundancy: 3.1 % / CC1/2: 0.981 / Rmerge(I) obs: 0.175 / Rpim(I) all: 0.173 / Rrim(I) all: 0.247 / Net I/σ(I): 3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
8.22-32.273.40.0552370.9840.0550.077
1.5-1.532.91.72716680.2331.7082.43

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Processing

Software
NameVersionClassification
REFMAC5.8.0266refinement
DIALSdata collection
Aimless0.7.4data reduction
Aimless0.7.4data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4tw7

4tw7


Resolution: 1.85→32.27 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.877 / SU B: 6.671 / SU ML: 0.095 / Cross valid method: THROUGHOUT / ESU R Free: 0.037
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2671 911 4.932 %
Rwork0.1827 17559 -
all0.187 --
obs-18470 96.803 %
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: 16.591 Å2
Baniso -1Baniso -2Baniso -3
1-5.848 Å20 Å2-0.953 Å2
2---4.62 Å2-0 Å2
3----1.228 Å2
Refinement stepCycle: LAST / Resolution: 1.85→32.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1878 0 112 42 2032
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0142040
X-RAY DIFFRACTIONr_bond_other_d0.0050.0181942
X-RAY DIFFRACTIONr_angle_refined_deg1.6451.7212754
X-RAY DIFFRACTIONr_angle_other_deg1.271.6914492
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9195252
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.74724.20369
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.72515320
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.306153
X-RAY DIFFRACTIONr_chiral_restr0.0510.2263
X-RAY DIFFRACTIONr_chiral_restr_other1.0690.238
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022235
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02410
X-RAY DIFFRACTIONr_nbd_refined0.1860.2392
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1870.21856
X-RAY DIFFRACTIONr_nbtor_refined0.1610.2969
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0880.2854
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.282
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0180.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1370.218
X-RAY DIFFRACTIONr_nbd_other0.1680.277
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2230.27
X-RAY DIFFRACTIONr_mcbond_it1.7491.8621020
X-RAY DIFFRACTIONr_mcbond_other1.7431.8611016
X-RAY DIFFRACTIONr_mcangle_it2.2232.7921268
X-RAY DIFFRACTIONr_mcangle_other2.2242.7941267
X-RAY DIFFRACTIONr_scbond_it1.5121.8181020
X-RAY DIFFRACTIONr_scbond_other1.5121.8181021
X-RAY DIFFRACTIONr_scangle_it1.8992.7231486
X-RAY DIFFRACTIONr_scangle_other1.8982.7221487
X-RAY DIFFRACTIONr_lrange_it2.54221.5962215
X-RAY DIFFRACTIONr_lrange_other2.54121.5962216
X-RAY DIFFRACTIONr_rigid_bond_restr1.52733982
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.8980.253550.1441304X-RAY DIFFRACTION96.5885
1.898-1.950.375350.1921276X-RAY DIFFRACTION97.6173
1.95-2.0060.322810.1721228X-RAY DIFFRACTION97.6137
2.006-2.0680.34550.1451202X-RAY DIFFRACTION97.669
2.068-2.1360.239580.171157X-RAY DIFFRACTION98.301
2.136-2.2110.303660.1811121X-RAY DIFFRACTION98.0992
2.211-2.2940.23540.1761092X-RAY DIFFRACTION97.6982
2.294-2.3880.37570.224928X-RAY DIFFRACTION87.2454
2.388-2.4940.306440.2221014X-RAY DIFFRACTION98.3271
2.494-2.6150.294530.201966X-RAY DIFFRACTION98.6447
2.615-2.7560.283470.185919X-RAY DIFFRACTION98.3707
2.756-2.9230.274500.2895X-RAY DIFFRACTION98.8494
2.923-3.1240.295550.197799X-RAY DIFFRACTION98.6143
3.124-3.3740.275370.209732X-RAY DIFFRACTION94.2402
3.374-3.6950.181380.177645X-RAY DIFFRACTION90.2246
3.695-4.1290.221360.163660X-RAY DIFFRACTION99.7135
4.129-4.7650.213340.14572X-RAY DIFFRACTION99.1817
4.765-5.8270.2220.18470X-RAY DIFFRACTION98.2036
5.827-8.2040.239220.209355X-RAY DIFFRACTION90.4077
8.204-32.270.346120.183224X-RAY DIFFRACTION97.9253

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