1M8T

Structure of an acidic Phospholipase A2 from the venom of Ophiophagus hannah at 2.1 resolution from a hemihedrally twinned crystal form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.192 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure of a king cobra phospholipase A2 determined from a hemihedrally twinned crystal.

Xu, S.Gu, L.Wang, Q.Shu, Y.Song, S.Lin, Z.

(2003) Acta Crystallogr D Biol Crystallogr 59: 1574-1581

  • DOI: 10.1107/s0907444903014598
  • Primary Citation of Related Structures:  
    1M8T

  • PubMed Abstract: 
  • An acidic PLA(2) (OH APLA(2)-II) from the venom of Ophiophagus hannah (king cobra) shows greater phospholipase A(2) activity and weaker cardiotoxic and myotoxic activity than a homologous acidic PLA(2) from the same venom. The crystal of the enzyme belongs to space group P6(3) ...

    An acidic PLA(2) (OH APLA(2)-II) from the venom of Ophiophagus hannah (king cobra) shows greater phospholipase A(2) activity and weaker cardiotoxic and myotoxic activity than a homologous acidic PLA(2) from the same venom. The crystal of the enzyme belongs to space group P6(3). The crystals are invariably hemihedrally twinned, exhibiting perfect 622 Laue symmetry. The structure was determined by molecular replacement and refined using a hemihedral twinning program at 2.1 A resolution. The final model has reasonable stereochemistry and a crystallographic R factor of 19.5% (R(free) = 21.5%). The structure reveals the molecular arrangement and the mode of twinning. There are six independent molecules in the asymmetric unit. Owing to the presence of a non-crystallographic twofold parallel to the hemihedral twinning twofold, the molecular packing in the twinned crystal is extremely similar to that in an untwinned crystal for four of the molecules. This unique molecular arrangement may be related to the difficulty in recognizing the twinning. The structure was compared with the previously determined structure of a homologous acidic PLA(2) from the same source. The comparison shows structural changes that might be implicated in the increased catalytic activity and weakened toxicity.


    Related Citations: 
    • Preliminary crystallographic study of an acidic phospholipase A2 from Ophiophagus hannah (king cobra)
      Xu, S., Gu, L., Wang, Q., Shu, Y., Lin, Z.
      (2002) Acta Crystallogr D Biol Crystallogr 58: 1836

    Organizational Affiliation

    National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, People's Republic of China.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Phospholipase a2
A, B, C, D, E, F
A, B, C, D, E, F
119Ophiophagus hannahMutation(s): 0 
EC: 3.1.1.4
Membrane Entity: Yes 
UniProt
Find proteins for Q9DF33 (Ophiophagus hannah)
Explore Q9DF33 
Go to UniProtKB:  Q9DF33
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9DF33
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEZ
Query on HEZ

Download Ideal Coordinates CCD File 
H [auth A],
I [auth A],
J [auth A],
K [auth A],
M [auth B],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
M [auth B],
O [auth C],
P [auth C],
R [auth D],
S [auth D],
T [auth D]
HEXANE-1,6-DIOL
C6 H14 O2
XXMIOPMDWAUFGU-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
G [auth A],
L [auth B],
N [auth C],
Q [auth D],
U [auth E],
G [auth A],
L [auth B],
N [auth C],
Q [auth D],
U [auth E],
V [auth F]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.192 
  • Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 98.06α = 90
b = 98.06β = 90
c = 132.39γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
CNSrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-09-02
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance