[English] 日本語
Yorodumi
- PDB-2kot: Solution structure of S100A13 with a drug amlexanox -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2kot
TitleSolution structure of S100A13 with a drug amlexanox
ComponentsProtein S100-A13
KeywordsSIGNALING PROTEIN / S100A13 / Calcium / Phosphoprotein
Function / homology
Function and homology information


positive regulation of interleukin-1 alpha production / RAGE receptor binding / mast cell degranulation / fibroblast growth factor binding / positive regulation of cytokine production / calcium-dependent protein binding / protein transport / positive regulation of canonical NF-kappaB signal transduction / copper ion binding / lipid binding ...positive regulation of interleukin-1 alpha production / RAGE receptor binding / mast cell degranulation / fibroblast growth factor binding / positive regulation of cytokine production / calcium-dependent protein binding / protein transport / positive regulation of canonical NF-kappaB signal transduction / copper ion binding / lipid binding / positive regulation of cell population proliferation / calcium ion binding / nucleolus / perinuclear region of cytoplasm / protein homodimerization activity / extracellular space / zinc ion binding / extracellular region / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
S100/CaBP-9k-type, calcium binding, subdomain / S-100/ICaBP type calcium binding domain / S-100/ICaBP type calcium binding domain / EF-hand / Recoverin; domain 1 / EF-hand domain pair / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-ANW / Protein S100-A13
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing, DGSA-distance geometry simulated annealing,distance geometry,simulated annealing
Model detailsfewest violations, model 1
AuthorsRani, S.G. / Mohan, S.K. / Yu, C.
CitationJournal: Biochemistry / Year: 2010
Title: Molecular level interactions of S100A13 with amlexanox: inhibitor for the formation of multi-protein complex in non-classical pathway of the acidic fibroblast growth factor
Authors: Rani, S.G. / Mohan, S.K. / Yu, C.
History
DepositionSep 30, 2009Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Mar 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 1, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Protein S100-A13
B: Protein S100-A13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,5774
Polymers22,9802
Non-polymers5972
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)18 / 200structures with the least restraint violations
RepresentativeModel #1fewest violations

-
Components

#1: Protein Protein S100-A13 / S100 calcium-binding protein A13


Mass: 11490.193 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: S100A13 / Plasmid: pGEX-4T / Production host: Escherichia coli (E. coli) / References: UniProt: Q99584
#2: Chemical ChemComp-ANW / 2-amino-7-(1-methylethyl)-5-oxo-5H-chromeno[2,3-b]pyridine-3-carboxylic acid


Mass: 298.293 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H14N2O4 / Comment: antiinflammatory*YM

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1312D 1H-1H NOESY
1413D CBCA(CO)NH
1513D C(CO)NH
1613D HNCO
1713D HNCA
1813D HBHA(CO)NH
1913D H(CCO)NH
11013D (H)CCH-TOCSY
11113D 1H-15N NOESY
11213D 1H-13C NOESY
11313D 13C-filter NOESY

-
Sample preparation

DetailsContents: 1.2mM [U-100% 13C; U-100% 15N] Protein S100-A13, 1.2mM Amlexanox-2, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.2 mMProtein S100-A13[U-100% 13C; U-100% 15N]1
1.2 mMAmlexanox-21
Sample conditionsIonic strength: 0.1 / pH: 5.6 / Pressure: ambient / Temperature: 298 K

-
NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 700 MHz

-
Processing

NMR software
NameVersionDeveloperClassification
ARIA2.2Linge, O'Donoghue, Nilgesstructure solution
ARIA2.2Linge, O'Donoghue, Nilgespeak picking
SparkyGoddardchemical shift assignment
SparkyGoddardchemical shift calculation
VnmrJVariancollection
VnmrJVarianprocessing
TALOSCornilescu, Delaglio and Baxdata analysis
HADDOCK2Dr. A.M.J.J. Bonvindocking the aria calculated protein with ligand (amlexanox)
ARIA2.2Linge, O'Donoghue, Nilgesrefinement
RefinementMethod: simulated annealing, DGSA-distance geometry simulated annealing,distance geometry,simulated annealing
Software ordinal: 1 / Details: ARIA/CNS
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 200 / Conformers submitted total number: 18 / Representative conformer: 1

+
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