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- PDB-2kot: Solution structure of S100A13 with a drug amlexanox -

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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 / calcium ion binding / positive regulation of cell population proliferation / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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
Water0
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

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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 / Amlexanox


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

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Experimental details

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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

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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

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NMR measurement

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

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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

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