1OP2

Crystal Structure of AaV-SP-II, a Glycosylated Snake Venom Serine Proteinase from Agkistrodon acutus

• PDB DOI: https://doi.org/10.2210/pdb1OP2/pdb

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


• Deposited: 2003-03-04 Released: 2004-05-25 
• Deposition Author(s): Zhu, Z., Teng, M., Niu, L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.211 
• R-Value Work: 0.165 
• R-Value Observed: 0.165 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 25.67 kDa 
• Atom Count: 1,938 
• Modelled Residue Count: 234 
• Deposited Residue Count: 234 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Venom serine proteinase	A	234	Deinagkistrodon acutus	Mutation(s): 0  EC: 3.4.21
UniProt
Find proteins for Q9I8X1 (Deinagkistrodon acutus) Explore Q9I8X1  Go to UniProtKB:  Q9I8X1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	B [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
SO4	C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.211 
• R-Value Work: 0.165 
• R-Value Observed: 0.165 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 119.43	α = 90
b = 42.83	β = 99.61
c = 44.94	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: 2004-05-25 
Deposition Author(s): Zhu, Z., Teng, M., Niu, L.

Revision History  

• Version 1.0: 2004-05-25
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.3: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary