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

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Basic information

Entry
Database: PDB / ID: 9gpp
TitleThe FK1 domain of FKBP51 in complex with the macrocyclic SAFit analog 12c/o
ComponentsPeptidyl-prolyl cis-trans isomerase FKBP5
KeywordsISOMERASE / FKBP / Inhibitor / SAFIT / Macrocycle / Complex
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
: / Peptidyl-prolyl cis-trans isomerase FKBP5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsMeyners, C. / Buffa, V. / Walz, C. / 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: Conformational Plasticity and Binding Affinity Enhancement Controlled by Linker Derivatization in Macrocycles.
Authors: Buffa, V. / Walz, C. / Meyners, C. / Zheng, M. / Oki Sugiarto, W. / Repity, M. / Achaq, H. / Brudy, C. / Spiske, M. / Cica, 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 / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.name
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
A: Peptidyl-prolyl cis-trans isomerase FKBP5
B: Peptidyl-prolyl cis-trans isomerase FKBP5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1454
Polymers28,0082
Non-polymers1,1372
Water1,09961
1
A: Peptidyl-prolyl cis-trans isomerase FKBP5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5732
Polymers14,0041
Non-polymers5691
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Peptidyl-prolyl cis-trans isomerase FKBP5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5732
Polymers14,0041
Non-polymers5691
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.906, 48.906, 196.343
Angle α, β, γ (deg.)90, 90, 120
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: GLU / End label comp-ID: GLU / Auth seq-ID: 13 - 140 / Label seq-ID: 1 - 128

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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-A1INO / 3-cyclohexyl-19,20-dimethoxy-19-methyl-11,20-dioxa-5-aza-1lambda5-polona-1,19lambda5-dithia-18-azanida-1lambda5-stannapentacyclo[19.2.1.05,10.013,18.018,22]tetracosane-4,12-quinone


Mass: 568.704 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C31H44N4O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 61 / 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: 2.42 Å3/Da / Density % sol: 49.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 14% PEG3350, 0.2M ammonium acetate, 0.1M HEPES-NaOH pH 7.5, 10% glycol

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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 15, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.1→49.09 Å / Num. obs: 16713 / % possible obs: 99.3 % / Redundancy: 8.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.105 / Rpim(I) all: 0.051 / Rrim(I) all: 0.117 / Χ2: 1.04 / Net I/σ(I): 11.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
8.91-49.098.70.03732.12880.9990.0170.0410.6699.8
2.1-2.166.31.3211.513210.6870.7041.5110.9698.1

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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: 2.1→41.436 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.92 / SU B: 14.582 / SU ML: 0.18 / Cross valid method: THROUGHOUT / ESU R: 0.234 / ESU R Free: 0.211
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2777 815 4.893 %
Rwork0.217 15842 -
all0.22 --
obs-16657 99.226 %
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: 37.708 Å2
Baniso -1Baniso -2Baniso -3
1--1.075 Å2-0.538 Å2-0 Å2
2---1.075 Å20 Å2
3---3.488 Å2
Refinement stepCycle: LAST / Resolution: 2.1→41.436 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1856 0 82 61 1999
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0121986
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161824
X-RAY DIFFRACTIONr_angle_refined_deg1.7411.8112697
X-RAY DIFFRACTIONr_angle_other_deg0.5681.7374243
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.2235254
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.82714.37516
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.35410288
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.9521065
X-RAY DIFFRACTIONr_chiral_restr0.0750.2300
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022266
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02402
X-RAY DIFFRACTIONr_nbd_refined0.2120.2368
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1960.21617
X-RAY DIFFRACTIONr_nbtor_refined0.1770.21026
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0880.2995
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1680.271
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1330.24
X-RAY DIFFRACTIONr_nbd_other0.1350.229
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.3250.25
X-RAY DIFFRACTIONr_mcbond_it22.371022
X-RAY DIFFRACTIONr_mcbond_other22.371022
X-RAY DIFFRACTIONr_mcangle_it2.8984.2551274
X-RAY DIFFRACTIONr_mcangle_other2.8994.2551275
X-RAY DIFFRACTIONr_scbond_it2.1322.436964
X-RAY DIFFRACTIONr_scbond_other2.1312.435965
X-RAY DIFFRACTIONr_scangle_it3.294.4131423
X-RAY DIFFRACTIONr_scangle_other3.2894.4121424
X-RAY DIFFRACTIONr_lrange_it5.01522.0972162
X-RAY DIFFRACTIONr_lrange_other5.01721.952154
X-RAY DIFFRACTIONr_ncsr_local_group_10.0790.053544
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.079330.05009
12BX-RAY DIFFRACTIONLocal ncs0.079330.05009
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
2.1-2.1550.347620.29411290.29612160.9090.92397.94410.291
2.155-2.2130.32510.27610970.27811740.90.93797.78530.268
2.213-2.2770.27530.26910640.26911280.9430.94699.02480.258
2.277-2.3470.272370.24510940.24611440.9370.95698.86360.233
2.347-2.4240.27510.2410080.24110730.9470.9698.69530.222
2.424-2.5090.324600.2419600.24610290.930.96199.12540.219
2.509-2.6030.391540.2169640.22510190.9070.96899.90190.197
2.603-2.7090.241410.239540.2310050.9740.96899.0050.206
2.709-2.8290.284440.2498830.259370.9420.95598.93280.224
2.829-2.9660.313610.2468130.2518760.9270.9699.77170.22
2.966-3.1260.277430.248350.2438790.9440.9699.88620.215
3.126-3.3140.424320.237940.2378280.8570.96299.75850.217
3.314-3.5410.269400.237460.2327860.9470.9691000.216
3.541-3.8230.229390.2086840.2097230.9760.9751000.2
3.823-4.1840.239340.1756430.1786770.9660.9831000.171
4.184-4.6720.247250.1515780.1546030.970.9871000.155
4.672-5.3840.241340.185330.1845690.9720.98299.64850.192
5.384-6.5660.234240.2214490.2224730.9740.9761000.221
6.566-9.1710.317220.1843670.193900.9370.98299.74360.202
9.171-41.4360.1580.2372470.2352560.9890.95799.60940.277
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)
13.0695-0.88560.68374.1433-0.56772.5556-0.0644-0.0242-0.082-0.29330.11860.31790.1251-0.1019-0.05420.1356-0.07630.00650.0582-0.00660.0326-18.4280.95893.4391
22.33570.39070.35154.0260.3422.6191-0.10270.02780.3915-0.16240.0346-0.2681-0.02950.08980.06810.0167-0.0165-0.00290.0911-0.00630.0953-8.727716.13428.6574
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA13 - 201
2X-RAY DIFFRACTION2ALLB13 - 201

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