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- PDB-1l3x: Solution Structure of Novel Disintegrin Salmosin -

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Basic information

Entry
Database: PDB / ID: 1l3x
TitleSolution Structure of Novel Disintegrin Salmosin
Componentsplatelet aggregation inhibitor disintegrin
KeywordsPROTEIN BINDING / Disintegrin / Snake Venome / RGD
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / metalloendopeptidase activity / toxin activity / proteolysis / extracellular region / metal ion binding / plasma membrane
Similarity search - Function
Disintegrin domain / Echistatin / Disintegrin, conserved site / Disintegrins signature. / Reprolysin domain, adamalysin-type / Reprolysin (M12B) family zinc metalloprotease / Disintegrin / Disintegrin domain profile. / Homologues of snake disintegrins / Disintegrin domain ...Disintegrin domain / Echistatin / Disintegrin, conserved site / Disintegrins signature. / Reprolysin domain, adamalysin-type / Reprolysin (M12B) family zinc metalloprotease / Disintegrin / Disintegrin domain profile. / Homologues of snake disintegrins / Disintegrin domain / Disintegrin domain superfamily / Peptidase M12B, ADAM/reprolysin / ADAM type metalloprotease domain profile. / Metallopeptidase, catalytic domain superfamily / Neutral zinc metallopeptidases, zinc-binding region signature. / Few Secondary Structures / Irregular
Similarity search - Domain/homology
Zinc metalloproteinase/disintegrin
Similarity search - Component
Biological speciesGloydius blomhoffi brevicaudus (short-tailed mamushi)
MethodSOLUTION NMR / distance geometry, simulated annealing
AuthorsShin, J. / Lee, W.
CitationJournal: Biochemistry / Year: 2003
Title: Solution structure of a novel disintegrin, salmosin, from Agkistrondon halys venom
Authors: Shin, J. / Hong, S.Y. / Chung, K. / Kang, I. / Jang, Y. / Kim, D.S. / Lee, W.
History
DepositionMar 1, 2002Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 23, 2003Provider: repository / Type: Initial release
SupersessionMar 2, 2004ID: 1IQ2
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 21, 2012Group: Other
Revision 1.4Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_nmr_software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: platelet aggregation inhibitor disintegrin


Theoretical massNumber of molelcules
Total (without water)7,7751
Polymers7,7751
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 90structures with the lowest energy
Representative

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Components

#1: Protein platelet aggregation inhibitor disintegrin / salmosin


Mass: 7774.694 Da / Num. of mol.: 1 / Fragment: residues 1-73 / Source method: isolated from a natural source
Source: (natural) Gloydius blomhoffi brevicaudus (short-tailed mamushi)
Species: Gloydius blomhoffi / Strain: brevicaudus / References: UniProt: Q90WC0
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
121DQF-COSY
1322D NOESY
142DQF-COSY

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Sample preparation

Details
Solution-IDContentsSolvent system
11mM Salmosin; 50mM phosphate buffer NA; 90% H2O, 10% D2O90% H2O/10% D2O
21mM Salmosin; 50mM phosphate buffer NA; 100% D2O100% D2O
Sample conditionsIonic strength: 50mM phosphate / pH: 7 / Pressure: 1 atm / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX5001
Bruker DRXBrukerDRX6002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6Brukercollection
XwinNMR2.6Brukerprocessing
NMRPipe1.8Delaglio,Fprocessing
Sparky3.1James,Tdata analysis
CNS1Brungerrefinement
RefinementMethod: distance geometry, simulated annealing / Software ordinal: 1
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 90 / Conformers submitted total number: 20

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