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

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Basic information

Entry
Database: PDB / ID: 9gpk
TitleThe FK1 domain of FKBP51 in complex with the macrocyclic SAFit analog 12c/j
ComponentsPeptidyl-prolyl cis-trans isomerase FKBP5
KeywordsISOMERASE / FKBP / Inhibitor / SAFIT / Macrocycle / Complex
Function / homology
Function and homology information


response to alcohol / 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 ...response to alcohol / 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 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 / 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
: / Peptidyl-prolyl cis-trans isomerase FKBP5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsMeyners, C. / Walz, C. / Buffa, V. / 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)29,1174
Polymers28,0082
Non-polymers1,1092
Water2,288127
1
A: Peptidyl-prolyl cis-trans isomerase FKBP5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5592
Polymers14,0041
Non-polymers5551
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)14,5592
Polymers14,0041
Non-polymers5551
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.872, 48.872, 195.79
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-A1INK / 2-cyclohexyl-1,19-dimethoxy-11,18-dioxa-1lambda5,19lambda5-diphospha-2-stannatetracyclo[18.2.1.01,6.06,10]tricosane-3,12-dione


Mass: 554.678 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C30H42N4O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 127 / 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: 2.41 Å3/Da / Density % sol: 48.96 %
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: May 20, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.75→48.95 Å / Num. obs: 28521 / % possible obs: 100 % / Redundancy: 10.6 % / CC1/2: 1 / Rmerge(I) obs: 0.055 / Rpim(I) all: 0.025 / Rrim(I) all: 0.061 / Χ2: 1.02 / Net I/σ(I): 20
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
9.09-48.958.30.0264.227310.0090.0220.6799.5
1.75-1.78111.5141.615080.6250.6821.6631.04100

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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: 1.75→42.36 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.919 / SU B: 6.202 / SU ML: 0.098 / Cross valid method: THROUGHOUT / ESU R: 0.125 / ESU R Free: 0.126
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2543 1378 4.844 %
Rwork0.2094 27071 -
all0.212 --
obs-28449 99.961 %
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: 40.199 Å2
Baniso -1Baniso -2Baniso -3
1--0.404 Å2-0.202 Å2-0 Å2
2---0.404 Å20 Å2
3---1.311 Å2
Refinement stepCycle: LAST / Resolution: 1.75→42.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1888 0 80 127 2095
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0122029
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161878
X-RAY DIFFRACTIONr_angle_refined_deg2.1341.812751
X-RAY DIFFRACTIONr_angle_other_deg0.7211.7434365
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.3755256
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.3381315
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.96810306
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.291073
X-RAY DIFFRACTIONr_chiral_restr0.1120.2299
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.022328
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02420
X-RAY DIFFRACTIONr_nbd_refined0.2090.2357
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1940.21734
X-RAY DIFFRACTIONr_nbtor_refined0.1810.21016
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0910.21087
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1590.2122
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0990.28
X-RAY DIFFRACTIONr_nbd_other0.1750.233
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2170.215
X-RAY DIFFRACTIONr_mcbond_it2.9362.3321027
X-RAY DIFFRACTIONr_mcbond_other2.932.3311027
X-RAY DIFFRACTIONr_mcangle_it3.7384.1881282
X-RAY DIFFRACTIONr_mcangle_other3.7394.1891283
X-RAY DIFFRACTIONr_scbond_it3.5842.5011002
X-RAY DIFFRACTIONr_scbond_other3.5822.5011003
X-RAY DIFFRACTIONr_scangle_it4.9484.4821469
X-RAY DIFFRACTIONr_scangle_other4.9474.4811470
X-RAY DIFFRACTIONr_lrange_it6.60423.5072247
X-RAY DIFFRACTIONr_lrange_other6.61123.1312220
X-RAY DIFFRACTIONr_ncsr_local_group_10.1040.053546
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.103750.05008
12BX-RAY DIFFRACTIONLocal ncs0.103750.05008
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
1.75-1.7950.327940.2619600.26320550.9240.94899.95130.257
1.795-1.8450.285890.25118860.25219750.9410.9521000.241
1.845-1.8980.2821060.22918650.23219710.9450.9631000.218
1.898-1.9560.2611090.22118240.22319330.9480.9661000.204
1.956-2.020.258800.22717440.22918240.9580.9641000.204
2.02-2.0910.263750.21716790.21917550.9560.96999.9430.195
2.091-2.170.27850.20416580.20817430.9560.9721000.182
2.17-2.2580.246670.18515930.18716600.960.9771000.163
2.258-2.3580.257880.20215330.20516210.9610.9741000.181
2.358-2.4730.305740.20214520.20615260.9460.9761000.178
2.473-2.6060.244700.19414000.19614700.9620.9781000.176
2.606-2.7640.19530.20313310.20213850.9760.97699.92780.186
2.764-2.9530.258540.2112560.21213110.9570.97299.92370.199
2.953-3.1890.208690.20811650.20812340.9720.9741000.203
3.189-3.4910.267560.22811210.23111780.9530.97399.91510.228
3.491-3.90.262450.229740.22210190.9550.9741000.226
3.9-4.4970.189630.178710.1719350.980.98499.8930.184
4.497-5.4920.261370.1767760.188130.960.981000.196
5.492-7.7020.265310.2486070.2496380.9560.9691000.273
7.702-42.360.342330.2583760.2664130.8830.93499.03150.286
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)
15.723-0.17731.08113.2098-0.10712.93220.36010.275-0.4827-0.2034-0.24010.26410.12720.1867-0.120.11890.0732-0.00980.0546-0.02520.0758-9.8672-15.4218-29.3986
23.0474-0.8710.05163.71420.62053.73680.04740.02810.433-0.2012-0.1840.2199-0.2755-0.0780.13670.0658-0.0012-0.00720.015-0.01760.099-18.41350.5302-4.145
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA13 - 201
2X-RAY DIFFRACTION2ALLB13 - 201

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