1BJJ | pdb_00001bjj

AGKISTRODOTOXIN, A PHOSPHOLIPASE A2-TYPE PRESYNAPTIC NEUROTOXIN FROM AGKISTRODON HALYS PALLAS

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 
    0.260 (Depositor) 
  • R-Value Work: 
    0.194 (Depositor) 
  • R-Value Observed: 
    0.194 (Depositor) 

Starting Model: experimental
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This is version 1.4 of the entry. See complete history. 

Literature

Structure of agkistrodotoxin in an orthorhombic crystal form with six molecules per asymmetric unit.

Tang, L., Zhou, Y.C., Lin, Z.J.

(1999) Acta Crystallogr D Biol Crystallogr 55: 1986-1996

  • DOI: https://doi.org/10.1107/s0907444999012603
  • Primary Citation Related Structures: 
    1BJJ

  • PubMed Abstract: 

    The structure of agkistrodotoxin crystallized under basic conditions has been determined at 2.8 A resolution by the molecular-replacement technique and refined to a crystallographic R factor of 0.194 and a free R factor of 0.260 with good stereochemistry. The molecular packing in the crystal differs from other PLA(2)s. The six molecules in the asymmetric unit form three dimers linked by Ca(2+) ions in a near-perfect six-ligand octahedral coordinating system. Extensive intermolecular hydrophobic interactions occur at the interfacial recognition site of each neurotoxin molecule, which provides an insight into phospholipase A(2)-membrane interactions. This hydrophobic interaction-induced molecular association along the interfacial recognition site suggests a self-protection mechanism of agkistrodotoxin.

    • Organizational Affiliation: 
    • National Laboratory of Biological Macromolecules, Institute of Biophysics, Academia Sinica, Beijing 100101, People's Republic of China.

Macromolecule Content 

  • Total Structure Weight: 84.4 kDa 
  • Atom Count: 5,857 
  • Modeled Residue Count: 732 
  • Deposited Residue Count: 732 
  • Unique protein chains: 1

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
AGKISTRODOTOXIN
A, B, C, D, E
A, B, C, D, E, F
122Gloydius halysMutation(s): 0 
EC: 3.1.1.4
UniProt
Find proteins for P14421 (Gloydius halys)
Explore P14421 
Go to UniProtKB:  P14421
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP14421
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free:  0.260 (Depositor) 
  • R-Value Work:  0.194 (Depositor) 
  • R-Value Observed: 0.194 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.75α = 90
b = 105.8β = 90
c = 110.03γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1999-07-29
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-08-02
    Changes: Database references, Derived calculations, Refinement description
  • Version 1.4: 2024-11-13
    Changes: Data collection, Structure summary