1UKM

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.196 

wwPDB Validation 3D Report Full Report


This is version 1.4 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
  • Also Cited By: 1V7P

  • 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 function ...

    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.(TOKYO) 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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
EMS16 A chain
A
134Echis multisquamatusMutation(s): 0 
Find proteins for Q7T2Q1 (Echis multisquamatus)
Go to UniProtKB:  Q7T2Q1
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
EMS16 B chain
B
128Echis multisquamatusMutation(s): 0 
Find proteins for Q7T2Q0 (Echis multisquamatus)
Go to UniProtKB:  Q7T2Q0
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.196 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 46.570α = 90.00
b = 59.933β = 90.00
c = 115.743γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-11-04
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance
  • Version 1.3: 2017-10-04
    Type: Refinement description
  • Version 1.4: 2018-07-25
    Type: Data collection, Database references, Structure summary