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

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Basic information

Entry
Database: PDB / ID: 7awx
TitleStructure of the FKBP51FK1 domain in complex with the macrocyclic SAFit analogue 55
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
Macrocyclic SAFit analogue 55 / Peptidyl-prolyl cis-trans isomerase FKBP5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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
DepositionNov 9, 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
B: Peptidyl-prolyl cis-trans isomerase FKBP5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4124
Polymers28,0082
Non-polymers1,4042
Water19811
1
A: Peptidyl-prolyl cis-trans isomerase FKBP5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,7062
Polymers14,0041
Non-polymers7021
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Peptidyl-prolyl cis-trans isomerase FKBP5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,7062
Polymers14,0041
Non-polymers7021
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.126, 64.621, 77.979
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.: 2
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-S5W / Macrocyclic SAFit analogue 55


Mass: 701.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C41H51NO9 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / 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: 2.25 Å3/Da / Density % sol: 45.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 40% PEG3350 0.1 M HEPES-NaOH pH 7.5 0.2M ammonium thiocyanate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 24, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→42.17 Å / Num. obs: 13332 / % possible obs: 99.5 % / Redundancy: 6.4 % / CC1/2: 0.997 / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.05 / Rrim(I) all: 0.094 / Net I/σ(I): 10
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
9.07-42.175.60.0462340.9970.0270.053
2.2-2.2761.12211380.8980.741.349

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Processing

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

4tw7


Resolution: 2.2→42.004 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.917 / SU B: 11.364 / SU ML: 0.264 / Cross valid method: THROUGHOUT / ESU R: 0.327 / ESU R Free: 0.266
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.303 655 4.929 %
Rwork0.2327 12634 -
all0.236 --
obs-13289 99.305 %
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: 53.947 Å2
Baniso -1Baniso -2Baniso -3
1--6.475 Å2-0 Å2-0 Å2
2--1.083 Å2-0 Å2
3---5.391 Å2
Refinement stepCycle: LAST / Resolution: 2.2→42.004 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1807 0 102 11 1920
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0131971
X-RAY DIFFRACTIONr_bond_other_d0.0060.0181803
X-RAY DIFFRACTIONr_angle_refined_deg1.6861.7162679
X-RAY DIFFRACTIONr_angle_other_deg1.5551.6844143
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.8335251
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.43822.67671
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.4515272
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.58156
X-RAY DIFFRACTIONr_chiral_restr0.0490.2262
X-RAY DIFFRACTIONr_chiral_restr_other1.6090.234
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022212
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02416
X-RAY DIFFRACTIONr_nbd_refined0.1960.2369
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1860.21712
X-RAY DIFFRACTIONr_nbtor_refined0.1750.2974
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.2879
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1230.250
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1990.27
X-RAY DIFFRACTIONr_nbd_other0.2340.228
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1840.23
X-RAY DIFFRACTIONr_mcbond_it4.1196.0831013
X-RAY DIFFRACTIONr_mcbond_other4.1126.0831012
X-RAY DIFFRACTIONr_mcangle_it6.1569.1211261
X-RAY DIFFRACTIONr_mcangle_other6.1559.121262
X-RAY DIFFRACTIONr_scbond_it3.6275.984958
X-RAY DIFFRACTIONr_scbond_other3.6255.983959
X-RAY DIFFRACTIONr_scangle_it5.3918.9231418
X-RAY DIFFRACTIONr_scangle_other5.398.9221419
X-RAY DIFFRACTIONr_lrange_it7.94970.4182117
X-RAY DIFFRACTIONr_lrange_other7.94970.4172117
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
2.2-2.2570.49480.4449110.4469630.4230.44499.58460.43
2.257-2.3190.448400.3849000.3879440.5260.53499.57630.369
2.319-2.3860.365400.3678800.3679240.6660.62299.56710.353
2.386-2.4590.373490.3238270.3268790.6540.70999.65870.309
2.459-2.5390.339450.2978190.2998680.770.78999.53920.281
2.539-2.6280.347490.2567980.2628500.80.84999.64710.245
2.628-2.7270.246340.2537690.2538030.8640.8841000.242
2.727-2.8380.277380.2517420.2527810.8450.87899.8720.24
2.838-2.9630.282420.2287180.2317610.8630.89299.86860.217
2.963-3.1070.292320.2346780.2377170.8590.90699.02370.226
3.107-3.2740.361300.2346500.2396980.8230.90597.42120.232
3.274-3.4720.311410.2545910.2586370.8610.88799.21510.257
3.472-3.7090.34300.2366010.2416360.8940.92499.21380.243
3.709-4.0040.277170.2045550.2075720.9220.9411000.221
4.004-4.3820.298300.1665020.1725360.8860.95799.25370.189
4.382-4.8930.23180.1724810.1744990.9170.961000.204
4.893-5.6370.299280.24080.2074370.9190.94899.77120.231
5.637-6.8730.234170.2333350.2333740.8990.93594.11760.273
6.873-9.5920.251200.1882810.1923050.9250.95998.68850.231
9.592-42.0040.28470.2621880.2621960.9650.93899.48980.321

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