[English] 日本語
Yorodumi
- PDB-6saf: The Fk1 domain of FKBP51 in complex with (S)-(R)-3-(3,4-dimethoxy... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6saf
TitleThe Fk1 domain of FKBP51 in complex with (S)-(R)-3-(3,4-dimethoxyphenyl)-1-(3-(2-morpholinoethoxy)phenyl)propyl 1-((1R,4aR,8aR)-4-oxodecahydronaphthalene-1-carbonyl)piperidine-2-carboxylate
ComponentsPeptidyl-prolyl cis-trans isomerase FKBP5
KeywordsCHAPERONE / Fk-506 binding domain / Hsp90 cochaperone / immunophiline / peptidyl-prolyl isomerase / ligand selectivity
Function / homology
Function and homology information


FK506 binding / MECP2 regulates neuronal receptors and channels / chaperone-mediated protein folding / heat shock protein binding / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / ESR-mediated signaling / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / response to bacterium / protein folding ...FK506 binding / MECP2 regulates neuronal receptors and channels / chaperone-mediated protein folding / heat shock protein binding / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / ESR-mediated signaling / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / response to bacterium / protein folding / protein-macromolecule adaptor activity / extracellular exosome / nucleoplasm / membrane / cytosol / cytoplasm
Similarity search - Function
: / Chitinase A; domain 3 - #40 / Tetratricopeptide repeat / Chitinase A; domain 3 / 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. ...: / Chitinase A; domain 3 - #40 / Tetratricopeptide repeat / Chitinase A; domain 3 / 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 / Roll / Alpha Beta
Similarity search - Domain/homology
Chem-L2Q / Peptidyl-prolyl cis-trans isomerase FKBP5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.05 Å
AuthorsFeng, X. / Sippel, C. / Knaup, F. / Bracher, A. / Staibano, S. / Romano, M.F. / Hausch, F.
Citation
Journal: J.Med.Chem. / Year: 2020
Title: A Novel Decalin-Based Bicyclic Scaffold for FKBP51-Selective Ligands.
Authors: Feng, X. / Sippel, C. / Knaup, F.H. / Bracher, A. / Staibano, S. / Romano, M.F. / Hausch, F.
#1: Journal: Acta Cryst. Sect. D / Year: 2011
Title: Structural characterization of the PPIase domain of FKBP51, a cochaperone of human Hsp90
Authors: Bracher, A. / Kozany, C. / Thost, A.K. / Hausch, F.
History
DepositionJul 16, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 18, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year / _citation_author.name
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)14,7172
Polymers14,0261
Non-polymers6911
Water1,20767
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.555, 50.334, 62.776
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
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: 14026.077 Da / Num. of mol.: 1 / Fragment: Fk1 domain
Mutation: additional N-terminal sequence GAP, cloning artefact, mutation A19T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FKBP5, AIG6, FKBP51 / Plasmid: pProEx-HtB / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): codon+ RIL / References: UniProt: Q13451, peptidylprolyl isomerase
#2: Chemical ChemComp-L2Q / [(1~{R})-3-(3,4-dimethoxyphenyl)-1-[3-(2-morpholin-4-ylethoxy)phenyl]propyl] (2~{S})-1-[[(1~{R},4~{a}~{R},8~{a}~{R})-4-oxidanylidene-2,3,4~{a},5,6,7,8,8~{a}-octahydro-1~{H}-naphthalen-1-yl]carbonyl]piperidine-2-carboxylate


Mass: 690.865 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C40H54N2O8 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 48.68 % / Mosaicity: 0.11 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 28 % PEG-3350, 0.2 M NH4-acetate and 0.1 M HEPES-NaOH pH 7.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97857 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 13, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.05→39.27 Å / Num. all: 8890 / Num. obs: 8890 / % possible obs: 99.7 % / Redundancy: 5.3 % / Biso Wilson estimate: 34 Å2 / Rpim(I) all: 0.031 / Rrim(I) all: 0.072 / Rsym value: 0.065 / Net I/av σ(I): 7.7 / Net I/σ(I): 13.3 / Num. measured all: 47289
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
2.05-2.165.40.5971.3679412530.2780.660.5972.599.6
2.16-2.295.10.4221.8615612120.2040.470.4223.499.6
2.29-2.455.60.2822.7633611260.1290.3110.2825.299.6
2.45-2.655.50.1814.1586710580.0840.20.1817.699.8
2.65-2.95.30.119651749760.0570.1330.11910.999.6
2.9-3.245.40.0769.248768980.0350.0840.07616.699.9
3.24-3.745.40.0512.742817910.0230.0560.0525.2100
3.74-4.584.90.03715.834476970.0180.0410.03731.599.8
4.58-6.485.30.03515.928975480.0170.0390.03533.9100
6.48-50.3344.40.0361214613310.0190.0410.03634.198.8

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation39.27 Å3 Å

-
Processing

Software
NameVersionClassification
XDSVERSION January 10, 2014data reduction
SCALA3.3.20data scaling
MOLREP11.0.05phasing
REFMAC5.8.0155refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdbid 3O5Q

3o5q


Resolution: 2.05→30 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.926 / SU B: 15.757 / SU ML: 0.177 / SU R Cruickshank DPI: 0.2068 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.207 / ESU R Free: 0.206
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2731 423 4.8 %RANDOM
Rwork0.1903 ---
obs0.194 8428 99.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 98.46 Å2 / Biso mean: 48.131 Å2 / Biso min: 24.74 Å2
Baniso -1Baniso -2Baniso -3
1-3.96 Å2-0 Å20 Å2
2---2.68 Å20 Å2
3----1.27 Å2
Refinement stepCycle: final / Resolution: 2.05→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms979 0 50 67 1096
Biso mean--50.24 58.28 -
Num. residues----128
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.021054
X-RAY DIFFRACTIONr_bond_other_d0.0080.021023
X-RAY DIFFRACTIONr_angle_refined_deg1.8572.0251417
X-RAY DIFFRACTIONr_angle_other_deg1.453.0222383
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5715127
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.424.87239
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.37215182
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.008153
X-RAY DIFFRACTIONr_chiral_restr0.0880.2150
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211141
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02214
LS refinement shellResolution: 2.05→2.103 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 33 -
Rwork0.335 597 -
all-630 -
obs--99.21 %
Refinement TLS params.Method: refined / Origin x: 5.3908 Å / Origin y: 2.1914 Å / Origin z: 18.7297 Å
111213212223313233
T0.0421 Å2-0.0175 Å2-0.0005 Å2-0.038 Å2-0.007 Å2--0.013 Å2
L3.951 °2-1.1536 °20.8689 °2-7.0216 °2-0.1054 °2--4.1659 °2
S-0.0875 Å °-0.1918 Å °-0.0246 Å °0.1359 Å °0.1346 Å °-0.2759 Å °0.0803 Å °0.1296 Å °-0.0471 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A13 - 140
2X-RAY DIFFRACTION1A201
3X-RAY DIFFRACTION1A301 - 367

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more