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- PDB-9gq7: The FK1 domain of FKBP51 in complex with the macrocyclic SAFit an... -

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Basic information

Entry
Database: PDB / ID: 9gq7
TitleThe FK1 domain of FKBP51 in complex with the macrocyclic SAFit analog p5(2,1)-(E)
ComponentsPeptidyl-prolyl cis-trans isomerase FKBP5
KeywordsISOMERASE / FKBP / Inhibitor / SAFIT / Macrocycle / Complex
Function / homology
Function and homology information


response to alcohol / Modulation of host responses by IFN-stimulated genes / FK506 binding / 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 / peptidyl-prolyl cis-trans isomerase activity / RNA polymerase II CTD heptapeptide repeat P3 isomerase activity ...response to alcohol / Modulation of host responses by IFN-stimulated genes / FK506 binding / 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 / peptidyl-prolyl cis-trans isomerase activity / RNA polymerase II CTD heptapeptide repeat P3 isomerase activity / RNA polymerase II CTD heptapeptide repeat P6 isomerase activity / peptidylprolyl isomerase / response to bacterium / response to cocaine / protein folding / protein-macromolecule adaptor activity / extracellular exosome / nucleoplasm / membrane / cytosol / cytoplasm
Similarity search - Function
: / Tetratricopeptide repeat / Tetratricopeptide repeat / FKBP-type peptidyl-prolyl cis-trans isomerase domain profile. / FKBP-type peptidyl-prolyl cis-trans isomerase / FKBP-type peptidyl-prolyl cis-trans isomerase domain / Peptidyl-prolyl cis-trans isomerase domain superfamily / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats ...: / Tetratricopeptide repeat / Tetratricopeptide repeat / FKBP-type peptidyl-prolyl cis-trans isomerase domain profile. / FKBP-type peptidyl-prolyl cis-trans isomerase / FKBP-type peptidyl-prolyl cis-trans isomerase domain / 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
: / Peptidyl-prolyl cis-trans isomerase FKBP5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsMeyners, C. / Spiske, M. / Hausch, F.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Federal Ministry for Education and Research03VP08671 Germany
German Research Foundation (DFG)525512762 Germany
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2025
Title: Conformationally Restricted Macrocycles as Improved FKBP51 Inhibitors Enabled by Systematic Linker Derivatization.
Authors: Spiske, M. / Meyners, C. / Bauder, M. / Repity, M. / Brudy, C. / Sugiarto, W.O. / Achaq, H. / Geiger, T.M. / Hausch, F.
History
DepositionSep 9, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 15, 2025Provider: repository / Type: Initial release
Revision 1.1Mar 12, 2025Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Mar 19, 2025Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)28,9514
Polymers28,0082
Non-polymers9432
Water45025
1
B: Peptidyl-prolyl cis-trans isomerase FKBP5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,4762
Polymers14,0041
Non-polymers4721
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Peptidyl-prolyl cis-trans isomerase FKBP5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,4762
Polymers14,0041
Non-polymers4721
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.482, 48.482, 191.085
Angle α, β, γ (deg.)90, 90, 120
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: GLY / End label comp-ID: GLY / Auth seq-ID: 17 - 139 / Label seq-ID: 5 - 127

Dom-IDAuth asym-IDLabel asym-ID
1BA
2AB

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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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 / 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-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q13451, peptidylprolyl isomerase
#2: Chemical ChemComp-A1IN5 / (2~{S},9~{S},14~{E})-2-cyclohexyl-19,22-dimethoxy-11,17-dioxa-4-azatricyclo[16.2.2.0^{4,9}]docosa-1(20),14,18,21-tetraene-3,10-dione


Mass: 471.586 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H37NO6 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.31 Å3/Da / Density % sol: 46.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 20% PEG3350, 0.2M ammonium thiocyanate, 0.1M 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 PILATUS3 S 6M / Detector: PIXEL / Date: Mar 18, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.02→41.99 Å / Num. obs: 18014 / % possible obs: 100 % / Redundancy: 10 % / CC1/2: 0.999 / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.036 / Rrim(I) all: 0.084 / Χ2: 0.98 / Net I/σ(I): 13.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
9.03-41.998.10.03137.92680.9990.0140.0340.6299.3
2.02-2.07111.3361.512640.530.6021.4680.75100

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Processing

Software
NameVersionClassification
REFMAC5.8.0430 (refmacat 0.4.82)refinement
autoXDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→41.99 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.902 / SU B: 19.437 / SU ML: 0.216 / Cross valid method: THROUGHOUT / ESU R: 0.359 / ESU R Free: 0.251
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2637 627 5.091 %
Rwork0.2206 11690 -
all0.223 --
obs-12317 99.927 %
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: 54.973 Å2
Baniso -1Baniso -2Baniso -3
1--1.117 Å2-0.559 Å2-0 Å2
2---1.117 Å20 Å2
3---3.625 Å2
Refinement stepCycle: LAST / Resolution: 2.3→41.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1833 0 68 25 1926
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0121946
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161762
X-RAY DIFFRACTIONr_angle_refined_deg2.0651.8122642
X-RAY DIFFRACTIONr_angle_other_deg0.6781.7334099
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8295250
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.10213.33318
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg2.78252
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.2610281
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.0331068
X-RAY DIFFRACTIONr_chiral_restr0.0910.2294
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022247
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02401
X-RAY DIFFRACTIONr_nbd_refined0.2070.2361
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2050.21607
X-RAY DIFFRACTIONr_nbtor_refined0.1820.2993
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0920.2998
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1640.255
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0110.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1910.211
X-RAY DIFFRACTIONr_nbd_other0.2020.226
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0390.21
X-RAY DIFFRACTIONr_mcbond_it4.1153.4991006
X-RAY DIFFRACTIONr_mcbond_other4.1093.4991006
X-RAY DIFFRACTIONr_mcangle_it5.6486.2861254
X-RAY DIFFRACTIONr_mcangle_other5.6476.2881255
X-RAY DIFFRACTIONr_scbond_it4.2973.6940
X-RAY DIFFRACTIONr_scbond_other4.2953.6941
X-RAY DIFFRACTIONr_scangle_it5.9766.551388
X-RAY DIFFRACTIONr_scangle_other5.9746.5481389
X-RAY DIFFRACTIONr_lrange_it7.58232.9722098
X-RAY DIFFRACTIONr_lrange_other7.57832.9662098
X-RAY DIFFRACTIONr_ncsr_local_group_10.1150.053343
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11BX-RAY DIFFRACTIONLocal ncs0.114980.05008
12AX-RAY DIFFRACTIONLocal ncs0.114980.05008
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
2.3-2.360.389510.3158190.3198710.9130.93699.88520.3
2.36-2.4240.375420.2818480.2858900.9170.9481000.266
2.424-2.4940.265370.2547720.2558090.9330.9571000.234
2.494-2.5710.29390.2137910.2178300.9480.9681000.198
2.571-2.6540.327540.2467230.2527770.9250.9591000.23
2.654-2.7470.384370.277370.2767740.9270.9511000.254
2.747-2.850.367350.2477360.2537710.9150.9541000.233
2.85-2.9660.405340.2456620.2536960.8870.9571000.235
2.966-3.0980.277380.2326470.2356860.9530.9699.85420.225
3.098-3.2480.319300.2446550.2476850.9180.9551000.243
3.248-3.4220.261290.2395830.246120.9560.9631000.239
3.422-3.6280.228370.2435690.2426060.960.9681000.248
3.628-3.8770.21300.2265390.2255690.9810.9741000.229
3.877-4.1850.212320.1955140.1965460.9760.9791000.206
4.185-4.5790.212310.1484640.1514980.9660.98699.39760.161
4.579-5.1120.167120.1474360.1474480.9840.9861000.163
5.112-5.8890.212190.193960.1914150.9690.9771000.206
5.889-7.1770.285150.2263440.2283590.9560.9751000.247
7.177-10.0050.19130.2362750.2342890.980.96699.6540.278
10.005-41.990.373120.3071760.3111900.890.92798.94740.386
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.5878-1.6884-0.5496.3877-0.3713.8854-0.1554-0.0703-0.0616-0.27670.1514-0.5774-0.240.19740.0040.1612-0.0842-0.02340.05020.02080.101318.60.9193.3835
23.22960.7735-0.46843.742-1.2953.1563-0.1311-0.0068-0.42180.18750.02540.15390.18160.01410.10570.21870.02750.02320.05910.03070.09779.3384-15.63928.0149
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLB13 - 201
2X-RAY DIFFRACTION2ALLA17 - 201

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