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

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Basic information

Entry
Database: PDB / ID: 9gpy
TitleThe FK1 domain of FKBP51 in complex with the macrocyclic SAFit analog 12g/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: 1.5 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
C: Peptidyl-prolyl cis-trans isomerase FKBP5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,9049
Polymers42,0123
Non-polymers1,8926
Water5,314295
1
A: Peptidyl-prolyl cis-trans isomerase FKBP5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6353
Polymers14,0041
Non-polymers6312
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)14,6353
Polymers14,0041
Non-polymers6312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Peptidyl-prolyl cis-trans isomerase FKBP5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6353
Polymers14,0041
Non-polymers6312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.589, 48.797, 99.904
Angle α, β, γ (deg.)90, 111.259, 90
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
32A
42C
53B
63C

NCS domain segments:

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-IDComponent-IDEns-IDAuth asym-IDLabel asym-ID
111AA
211BB
322AA
422CC
533BB
633CC

NCS ensembles :
IDDetails
1Local NCS retraints between domains: 1 2
2Local NCS retraints between domains: 3 4
3Local NCS retraints between domains: 5 6

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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.: 3 / 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-A1INZ / 2-cyclohexyl-18,19-dimethoxy-13-methyl-11,17-dioxa-4-aza-1lambda5,18lambda5-diphospha-1,15-distannatetracyclo[13.4.0.04,9.016,20]nonadecane-3,10-quinone


Mass: 568.704 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C31H44N4O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 295 / 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: 2.29 Å3/Da / Density % sol: 46.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 18% 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: Jun 26, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.5→46.55 Å / Num. obs: 60091 / % possible obs: 98.5 % / Redundancy: 5.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.038 / Rrim(I) all: 0.065 / Χ2: 1.01 / Net I/σ(I): 12.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
8.22-46.555.10.01739.539510.0120.0210.7198
1.5-1.535.51.5731.129660.6661.1191.9391.0296.8

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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: 1.5→46.55 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.963 / SU B: 5.111 / SU ML: 0.077 / Cross valid method: THROUGHOUT / ESU R: 0.094 / ESU R Free: 0.081
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.22 3029 5.041 %
Rwork0.1748 57059 -
all0.177 --
obs-60088 98.455 %
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: 20.9 Å2
Baniso -1Baniso -2Baniso -3
1-0.969 Å20 Å2-2.037 Å2
2---0.471 Å2-0 Å2
3---0.835 Å2
Refinement stepCycle: LAST / Resolution: 1.5→46.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2825 0 135 295 3255
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0123093
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162900
X-RAY DIFFRACTIONr_angle_refined_deg1.6581.8224187
X-RAY DIFFRACTIONr_angle_other_deg0.5571.7446754
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9745393
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.50413.65426
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.14210486
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.36610104
X-RAY DIFFRACTIONr_chiral_restr0.0830.2456
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023524
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02626
X-RAY DIFFRACTIONr_nbd_refined0.2070.2526
X-RAY DIFFRACTIONr_symmetry_nbd_other0.20.22502
X-RAY DIFFRACTIONr_nbtor_refined0.1780.21559
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0910.21525
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1380.2195
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.160.212
X-RAY DIFFRACTIONr_nbd_other0.1810.264
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1050.232
X-RAY DIFFRACTIONr_mcbond_it7.2052.0291563
X-RAY DIFFRACTIONr_mcbond_other7.1962.0281563
X-RAY DIFFRACTIONr_mcangle_it10.613.6421959
X-RAY DIFFRACTIONr_mcangle_other10.6153.6431960
X-RAY DIFFRACTIONr_scbond_it7.3872.0731530
X-RAY DIFFRACTIONr_scbond_other7.3852.0731531
X-RAY DIFFRACTIONr_scangle_it10.6423.7192228
X-RAY DIFFRACTIONr_scangle_other10.643.722229
X-RAY DIFFRACTIONr_lrange_it15.64721.553432
X-RAY DIFFRACTIONr_lrange_other15.09720.8333378
X-RAY DIFFRACTIONr_rigid_bond_restr5.02635993
X-RAY DIFFRACTIONr_ncsr_local_group_10.0770.053708
X-RAY DIFFRACTIONr_ncsr_local_group_20.0820.053674
X-RAY DIFFRACTIONr_ncsr_local_group_30.080.053631
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.076530.05009
12BX-RAY DIFFRACTIONLocal ncs0.076530.05009
23AX-RAY DIFFRACTIONLocal ncs0.08190.05009
24CX-RAY DIFFRACTIONLocal ncs0.08190.05009
35BX-RAY DIFFRACTIONLocal ncs0.079610.05009
36CX-RAY DIFFRACTIONLocal ncs0.079610.05009
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
1.5-1.5390.3632230.34842010.34945300.870.86797.660.338
1.539-1.5810.3122280.30940050.30943450.9040.90397.42230.297
1.581-1.6270.3072310.27539500.27742780.8850.92497.73260.256
1.627-1.6770.2692070.25538310.25641120.9180.93498.20040.236
1.677-1.7320.2621960.2336850.23139720.9250.94797.7090.207
1.732-1.7920.2241690.17536550.17838750.9580.97598.68390.155
1.792-1.860.2151700.15835150.16137350.9670.98298.66130.138
1.86-1.9360.1951560.15234130.15436130.9720.98598.78220.131
1.936-2.0220.2091600.14432770.14734750.9690.98798.90650.124
2.022-2.120.2291460.1431280.14333240.9690.98998.49580.122
2.12-2.2350.1811690.13129140.13431330.9810.9998.40410.116
2.235-2.370.1971480.14727800.1529440.9730.98799.45650.132
2.37-2.5330.2081640.14726570.15128360.9720.98899.47110.135
2.533-2.7350.1981370.1524550.15226110.9770.98799.27230.14
2.735-2.9950.2141030.16422680.16624050.9750.98398.58630.156
2.995-3.3470.255990.17820350.18221850.9680.98297.66590.177
3.347-3.8620.2191060.16918350.17219520.9770.98799.43650.175
3.862-4.7210.165930.14315480.14416450.9880.98999.75680.16
4.721-6.6430.215780.17912010.18112970.9820.98798.61220.203
6.643-46.550.269460.2487060.257630.9590.97698.55830.297

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