[English] 日本語
Yorodumi
- PDB-8chm: Human FKBP12 in complex with (1S,5S,6R)-10-((S)-(3,5-dichlorophen... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8chm
TitleHuman FKBP12 in complex with (1S,5S,6R)-10-((S)-(3,5-dichlorophenyl)sulfinyl)-3-(pyridin-2-ylmethyl)-5-vinyl-3,10-diazabicyclo[4.3.1]decan-2-one
ComponentsPeptidyl-prolyl cis-trans isomerase FKBP1A
KeywordsISOMERASE / FKBP12 / Inhibitor
Function / homology
Function and homology information


macrolide binding / activin receptor binding / regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion / cytoplasmic side of membrane / transforming growth factor beta receptor binding / signaling receptor inhibitor activity / TGFBR1 LBD Mutants in Cancer / type I transforming growth factor beta receptor binding / negative regulation of activin receptor signaling pathway / heart trabecula formation ...macrolide binding / activin receptor binding / regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion / cytoplasmic side of membrane / transforming growth factor beta receptor binding / signaling receptor inhibitor activity / TGFBR1 LBD Mutants in Cancer / type I transforming growth factor beta receptor binding / negative regulation of activin receptor signaling pathway / heart trabecula formation / I-SMAD binding / regulation of amyloid precursor protein catabolic process / terminal cisterna / ryanodine receptor complex / ventricular cardiac muscle tissue morphogenesis / protein maturation by protein folding / 'de novo' protein folding / FK506 binding / channel regulator activity / TGF-beta receptor signaling activates SMADs / mTORC1-mediated signalling / protein peptidyl-prolyl isomerization / Calcineurin activates NFAT / regulation of immune response / regulation of ryanodine-sensitive calcium-release channel activity / heart morphogenesis / supramolecular fiber organization / sarcoplasmic reticulum membrane / T cell activation / sarcoplasmic reticulum / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / negative regulation of transforming growth factor beta receptor signaling pathway / calcium ion transmembrane transport / Z disc / SARS-CoV-1 activates/modulates innate immune responses / positive regulation of protein binding / protein folding / regulation of protein localization / protein refolding / positive regulation of canonical NF-kappaB signal transduction / transmembrane transporter binding / amyloid fibril formation / Potential therapeutics for SARS / membrane / cytosol / cytoplasm
Similarity search - Function
: / 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
Similarity search - Domain/homology
: / Chem-UT6 / Peptidyl-prolyl cis-trans isomerase FKBP1A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.12 Å
AuthorsMeyners, C. / Purder, P.L. / Hausch, F.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Federal Ministry for Education and Research Germany
CitationJournal: Jacs Au / Year: 2023
Title: Deconstructing Protein Binding of Sulfonamides and Sulfonamide Analogues.
Authors: Purder, P.L. / Meyners, C. / Sugiarto, W.O. / Kolos, J. / Lohr, F. / Gebel, J. / Nehls, T. / Dotsch, V. / Lermyte, F. / Hausch, F.
History
DepositionFeb 8, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 6, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Peptidyl-prolyl cis-trans isomerase FKBP1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,90912
Polymers11,8321
Non-polymers1,07611
Water3,855214
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)35.592, 40.081, 91.212
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Peptidyl-prolyl cis-trans isomerase FKBP1A / PPIase FKBP1A / 12 kDa FK506-binding protein / 12 kDa FKBP / FKBP-12 / Calstabin-1 / FK506-binding ...PPIase FKBP1A / 12 kDa FK506-binding protein / 12 kDa FKBP / FKBP-12 / Calstabin-1 / FK506-binding protein 1A / FKBP-1A / Immunophilin FKBP12 / Rotamase


Mass: 11832.496 Da / Num. of mol.: 1 / Mutation: C22V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FKBP1A, FKBP1, FKBP12 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P62942, peptidylprolyl isomerase

-
Non-polymers , 6 types, 225 molecules

#2: Chemical ChemComp-UT6 / (1~{S},5~{S},6~{R})-10-[3,5-bis(chloranyl)phenyl]sulfinyl-5-ethenyl-3-(pyridin-2-ylmethyl)-3,10-diazabicyclo[4.3.1]decan-2-one


Mass: 464.408 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H23Cl2N3O2S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cd
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 214 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.75 Å3/Da / Density % sol: 55.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 2.1 M ammonium sulfate, 0.2 M cadmium chloride, 0.1M HEPES-NaOH pH 7.5

-
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: Sep 10, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.12→45.648 Å / Num. obs: 50936 / % possible obs: 99.7 % / Redundancy: 7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.026 / Rpim(I) all: 0.015 / Rrim(I) all: 0.03 / Net I/σ(I): 30.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
6.13-45.616.10.0293820.9990.0170.034
1.12-1.147.20.09624760.9960.0560.111

-
Processing

Software
NameVersionClassification
REFMAC5.8.0403refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.12→45.648 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.97 / SU B: 0.556 / SU ML: 0.013 / Cross valid method: THROUGHOUT / ESU R: 0.025 / ESU R Free: 0.025
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1455 2537 4.988 %
Rwork0.13 48329 -
all0.131 --
obs-50866 99.626 %
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: 10.321 Å2
Baniso -1Baniso -2Baniso -3
1-1.555 Å20 Å20 Å2
2---0.7 Å2-0 Å2
3----0.855 Å2
Refinement stepCycle: LAST / Resolution: 1.12→45.648 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms814 0 47 214 1075
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.012898
X-RAY DIFFRACTIONr_bond_other_d0.0060.016824
X-RAY DIFFRACTIONr_angle_refined_deg1.8781.7071225
X-RAY DIFFRACTIONr_angle_other_deg0.8641.6191901
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0595112
X-RAY DIFFRACTIONr_dihedral_angle_2_deg4.00656
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.30610137
X-RAY DIFFRACTIONr_dihedral_angle_6_deg17.1611036
X-RAY DIFFRACTIONr_chiral_restr0.1650.2133
X-RAY DIFFRACTIONr_chiral_restr_other2.2310.25
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021054
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02201
X-RAY DIFFRACTIONr_nbd_refined0.2350.2145
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2030.2753
X-RAY DIFFRACTIONr_nbtor_refined0.1790.2435
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0890.2452
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2750.2133
X-RAY DIFFRACTIONr_metal_ion_refined0.1540.25
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2530.25
X-RAY DIFFRACTIONr_nbd_other0.1760.228
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.3350.223
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0990.21
X-RAY DIFFRACTIONr_mcbond_it0.6870.971445
X-RAY DIFFRACTIONr_mcbond_other0.6870.971444
X-RAY DIFFRACTIONr_mcangle_it0.8731.755558
X-RAY DIFFRACTIONr_mcangle_other0.8721.754559
X-RAY DIFFRACTIONr_scbond_it1.3371.171453
X-RAY DIFFRACTIONr_scbond_other1.3291.169450
X-RAY DIFFRACTIONr_scangle_it1.6592.053667
X-RAY DIFFRACTIONr_scangle_other1.6452.045662
X-RAY DIFFRACTIONr_lrange_it2.80814.6811080
X-RAY DIFFRACTIONr_lrange_other2.10711.038978
X-RAY DIFFRACTIONr_rigid_bond_restr5.01131722
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
1.12-1.1490.1181800.135200.10137300.9890.99399.19570.09
1.149-1.1810.1091730.09634090.09736070.9920.99499.30690.088
1.181-1.2150.1211710.09433600.09535510.9910.99499.43680.086
1.215-1.2520.1151840.09232090.09334120.9910.99599.44310.086
1.252-1.2930.1141520.09231590.09333320.9920.99599.36970.087
1.293-1.3390.1161530.09230680.09332250.9930.99599.8760.088
1.339-1.3890.1161590.09629400.09731040.9930.99499.83890.093
1.389-1.4460.1091520.09328420.09430080.9940.99599.53460.093
1.446-1.510.1141400.09627390.09628850.9920.99499.7920.099
1.51-1.5830.1071450.09826180.09927660.9930.99499.89150.103
1.583-1.6690.1191430.10224850.10326350.9910.99399.73430.113
1.669-1.770.1121180.10623620.10724830.9920.99399.87920.12
1.77-1.8920.1361100.11822490.11923650.9890.99199.74630.138
1.892-2.0430.121030.12621020.12522090.9910.99199.81890.151
2.043-2.2380.1591110.13419260.13520410.9850.98999.8040.164
2.238-2.5010.151990.14417460.14418470.9840.98799.89170.184
2.501-2.8870.17820.15915520.1616390.9810.98499.69490.207
2.887-3.5320.224640.17813550.1814240.9660.9899.64890.23
3.532-4.980.176660.15510520.15611210.9810.98599.73240.209
4.98-45.6480.193320.2146360.2136730.9840.96899.25710.324

+
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