3UBU

Crystal structure of agkisacucetin, a GpIb-binding snaclec (snake C-type lectin) that inhibits platelet


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.91 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.192 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Crystal structure of agkisacucetin, a Gpib-binding snake C-type lectin that inhibits platelet adhesion and aggregation.

Gao, Y.Ge, H.Chen, H.Li, H.Liu, Y.Chen, L.Li, X.Liu, J.Niu, L.Teng, M.

(2012) Proteins --: --

  • DOI: 10.1002/prot.24060

  • PubMed Abstract: 
  • Agkisacucetin is a snake C-type lectin isolated from the venom of Agkistrodon acutus (A. acutus). It binds specifically to the platelet glycoprotein (GP) Ib and prevents the von Willebrand factor (VWF) accessing it. We determined the crystal structur ...

    Agkisacucetin is a snake C-type lectin isolated from the venom of Agkistrodon acutus (A. acutus). It binds specifically to the platelet glycoprotein (GP) Ib and prevents the von Willebrand factor (VWF) accessing it. We determined the crystal structure of agkisacucetin to 1.9Å resolution. The structure of agkisacucetin has an (αβ) fold similar to another GPIb-binding protein, flavocetin-A, but lacks the C-terminal cysteine in the β-subunit, does not form (βα)(4) tetramers, and does not cluster GPIbs, like flavocetin-A.


    Organizational Affiliation

    Hefei National Laboratory for Physical Sciences at Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Agglucetin subunit alpha-1
A
131Deinagkistrodon acutusMutation(s): 0 
Find proteins for Q8JIV9 (Deinagkistrodon acutus)
Go to UniProtKB:  Q8JIV9
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Agglucetin subunit beta-2
B
126Deinagkistrodon acutusMutation(s): 0 
Find proteins for Q8AYA3 (Deinagkistrodon acutus)
Go to UniProtKB:  Q8AYA3
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
OCS
Query on OCS
B
L-PEPTIDE LINKINGC3 H7 N O5 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.91 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.192 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 30.485α = 90.00
b = 58.052β = 90.00
c = 141.537γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
HKL-2000data scaling
HKL-2000data reduction
REFMACrefinement
HKL-2000data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-04-11
    Type: Initial release