3UBU | pdb_00003ubu

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

• PDB DOI: https://doi.org/10.2210/pdb3UBU/pdb

• Classification: TOXIN
• Organism(s): Deinagkistrodon acutus
• Mutation(s): No 


• Deposited: 2011-10-25 Released: 2012-04-11 
• Deposition Author(s): Gao, Y., Ge, H., Chen, H., Li, H., Liu, Y., Niu, L., Teng, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.91 Å
• R-Value Free: 
  0.222 (Depositor), 0.307 (DCC) 
• R-Value Work: 
  0.192 (Depositor) 
• R-Value Observed: 
  0.193 (Depositor) 

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 

• PubMed: 22447656 
• DOI: https://doi.org/10.1002/prot.24060
• Primary Citation Related Structures: 
  3UBU


• 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 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.

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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.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 30.16 kDa 
• Atom Count: 2,239 
• Modeled Residue Count: 256 
• Deposited Residue Count: 257 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Agglucetin subunit alpha-1	A	131	Deinagkistrodon acutus	Mutation(s): 0
UniProt
Find proteins for Q8JIV9 (Deinagkistrodon acutus) Explore Q8JIV9  Go to UniProtKB:  Q8JIV9

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Agglucetin subunit beta-2	B	126	Deinagkistrodon acutus	Mutation(s): 0
UniProt
Find proteins for Q8AYA3 (Deinagkistrodon acutus) Explore Q8AYA3  Go to UniProtKB:  Q8AYA3

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	D [auth B], E [auth B], F [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
OCS	B	L-PEPTIDE LINKING	C3 H7 N O5 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.91 Å
• R-Value Free:  0.222 (Depositor), 0.307 (DCC) 
• R-Value Work:  0.192 (Depositor) 
• R-Value Observed: 0.193 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 30.485	α = 90
b = 58.052	β = 90
c = 141.537	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-04-11 
Deposition Author(s): Gao, Y., Ge, H., Chen, H., Li, H., Liu, Y., Niu, L., Teng, M.

Revision History  

• Version 1.0: 2012-04-11
  Type: Initial release
  
• Version 1.1: 2025-03-26
  Changes: Data collection, Database references, Derived calculations, Structure summary