1Y17

crystal structure of Aa-X-bp-II, a snake venom protein with the activity of binding to coagulation factor X from Agkistrodon acutus

• PDB DOI: https://doi.org/10.2210/pdb1Y17/pdb

• Classification: BLOOD CLOTTING
• Organism(s): Deinagkistrodon acutus
• Mutation(s): No 


• Deposited: 2004-11-17 Released: 2006-03-07 
• Deposition Author(s): Zhu, Z., Liu, S., Mo, X., Yu, X., Liang, Z., Zang, J., Zhao, W., Teng, M., Niu, L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.236 (Depositor), 0.237 (DCC) 
• R-Value Work: 
  0.180 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.180 (Depositor) 

Literature

Characterizations and Crystal structures of two snake venom proteins with the activity of binding coagulation factor X from Agkistrodon acutus

Zhu, Z., Liu, S., Mo, X., Yu, X., Liang, Z., Zang, J., Zhao, W., Teng, M., Niu, L.

To be published.

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: 29.37 kDa 
• Atom Count: 2,135 
• Modelled Residue Count: 252 
• Deposited Residue Count: 252 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
anticoagulant protein A	A	129	Deinagkistrodon acutus	Mutation(s): 0
UniProt
Find proteins for Q9DEF9 (Deinagkistrodon acutus) Explore Q9DEF9  Go to UniProtKB:  Q9DEF9

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
anticoagulant protein-B	B	123	Deinagkistrodon acutus	Mutation(s): 0
UniProt
Find proteins for Q9DEF8 (Deinagkistrodon acutus) Explore Q9DEF8  Go to UniProtKB:  Q9DEF8

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	C [auth A], D [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.236 (Depositor), 0.237 (DCC) 
• R-Value Work:  0.180 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.180 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 34.944	α = 90
b = 53.894	β = 98.39
c = 68.087	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-03-07 
Deposition Author(s): Zhu, Z., Liu, S., Mo, X., Yu, X., Liang, Z., Zang, J., Zhao, W., Teng, M., Niu, L.

Revision History  

• Version 1.0: 2006-03-07
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-11-13
  Changes: Data collection, Database references, Derived calculations, Structure summary