1UKM

Crystal structure of EMS16, an Antagonist of collagen receptor integrin alpha2beta1 (GPIa/IIa)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.196 

Starting Model: experimental
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This is version 1.6 of the entry. See complete history


Literature

Structural characterization of EMS16, an Antagonist of collagen receptor (GPIa/IIa) from the venom of Echis multisquamatus

Horii, K.Okuda, D.Morita, T.Mizuno, H.

(2003) Biochemistry 42: 12497-12502

  • DOI: https://doi.org/10.1021/bi034890h
  • Primary Citation of Related Structures:  
    1UKM

  • PubMed Abstract: 

    Snake venoms contain a number of hemostatically active C-type lectin-like proteins (CLPs), which affect the blood coagulation system, endothelial cells, and platelets. CLPs have broad similarities in structure and possess distinct biological functions. EMS16, a CLP from Echis multisquamatus venom, which is a potent and selective inhibitor of the collagen receptor, glycoprotein Ia/IIa (integrin alpha2beta1), has been used in the present study to examine structure-function relationships in venom CLPs by X-ray crystallography. The structure of EMS16, determined at a resolution of 1.9 A, revealed a heterodimer involved with domain swapping of the central loop as observed in the structures of other CLPs. A part of the glycan was observed and identified as N-acetyl-D-glucosamine (GlcNAc) in the electron density map at Asn21 of subunit B, an expected glycosylation site. EMS16 had a unique, positively charged electrostatic potential patch on the concave surface that may qualify as a site for interaction with the I-domain of the glycoprotein Ia/IIa.


  • Organizational Affiliation

    Department of Biochemistry, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
EMS16 A chain134Echis multisquamatusMutation(s): 0 
UniProt
Find proteins for Q7T2Q1 (Echis multisquamatus)
Explore Q7T2Q1 
Go to UniProtKB:  Q7T2Q1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7T2Q1
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
EMS16 B chain128Echis multisquamatusMutation(s): 0 
UniProt
Find proteins for Q7T2Q0 (Echis multisquamatus)
Explore Q7T2Q0 
Go to UniProtKB:  Q7T2Q0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7T2Q0
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.196 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.57α = 90
b = 59.933β = 90
c = 115.743γ = 90
Software Package:
Software NamePurpose
CNSrefinement
AMoREphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-11-04
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2017-10-04
    Changes: Refinement description
  • Version 1.4: 2018-07-25
    Changes: Data collection, Database references, Structure summary
  • Version 1.5: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.6: 2023-10-25
    Changes: Data collection, Database references, Refinement description, Structure summary