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 

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Ligand Structure Quality Assessment 


This is version 1.5 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: 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 ...

    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.


    Related Citations: 
    • Characterization and Preliminary Crystallographic Studies of EMS16, an Antagonist of Collagen Receptor (GPIa/IIa) from the Venom of Echis multisquamatus
      Okuda, D., Horii, K., Mizuno, H., Morita, T.
      (2003) J Biochem 134: 19
    • Isolation and characterization of EMS16, a C-lectin type protein from Echis multisquamatus venom, a potent and selective inhibitor of the alpha2beta1 integrin
      Marcinkiewicz, C., Lobb, R.R., Marcinkiewicz, M.M., Daniel, J.L., Smith, J.B., Dangelmaier, C., Weinreb, P.H., Beacham, D.A., Niewiarowski, S.
      (2000) Biochemistry 39: 9859

    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)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
EMS16 A chainA134Echis multisquamatusMutation(s): 0 
UniProt
Find proteins for Q7T2Q1 (Echis multisquamatus)
Explore Q7T2Q1 
Go to UniProtKB:  Q7T2Q1
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
EMS16 B chainB128Echis multisquamatusMutation(s): 0 
UniProt
Find proteins for Q7T2Q0 (Echis multisquamatus)
Explore Q7T2Q0 
Go to UniProtKB:  Q7T2Q0
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG (Subject of Investigation/LOI)
Query on NAG

Download Ideal Coordinates CCD File 
G [auth B]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
D [auth A], E [auth A], F [auth A], H [auth B]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
C [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
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