1M8R

Crystal Structures of Cadmium-binding Acidic Phospholipase A2 from the Venom of Agkistrodon halys pallas at 1.9 Resolution (crystal grown at pH 7.4)

Structural Biology Knowledgebase: 1M8R SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.210
  • R-Value Work: 0.193

Literature

Macromolecules
Sequence Display for 1M8R

Classification: Hydrolase

Total Structure Weight: 14249.39

Macromolecule Entities
Molecule Chains Length Organism Details
phospholipase A2 A 124 Gloydius halys EC#: 3.1.1.4 IUBMB
Mutation: I3V, F20Q, T111N, L112T
Gene Name(s):
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 2 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
CD
Query on CD

A CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
BU1
Query on BU1

A 1,4-BUTANEDIOL
C4 H10 O2
WERYXYBDKMZEQL-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.210
  • R-Value Work: 0.193
  • Space Group: P 61
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 83.27 α = 90.00
b = 83.27 β = 90.00
c = 32.80 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2002-07-25
  • Released Date: 2003-02-11
  • Deposition author(s): Xu, S., Gu, L., Zhou, Y., Lin, Z.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4