1KPM

First Structural Evidence of a Specific Inhibition of Phospholipase A2 by Vitamin E and its Implications in Inflammation: Crystal Structure of the Complex Formed between Phospholipase A2 and Vitamin E at 1.8 A Resolution.

Structural Biology Knowledgebase: 1KPM SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.228
  • R-Value Work: 0.197

Literature

Macromolecules
Sequence Display for 1KPM

Classification: HYDROLASE

Total Structure Weight: 27930.54

Macromolecule Entities
Molecule Chains Length Organism Details
Phospholipase A2 A, B 121 Daboia russelii EC#: 3.1.1.4 IUBMB
Gene Name(s):
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A VITAMIN E
2,5,7,8-TETRAMETHYL-2-(4,8,12-TRIMETHYLTRIDECYL)- 6-CHROMANOL (Synonym)
C29 H50 O2
GVJHHUAWPYXKBD-SYZUXVNWSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ACY
Query on ACY

A, B ACETIC ACID
C2 H4 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
VIT N/A in BindingDB
Ki: 1590 nM  BindingMOAD
Ki: 1590 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.228
  • R-Value Work: 0.197
  • Space Group: C 2 2 21

Unit Cell:

Length (Å) Angle (°)
a = 75.79 α = 90.00
b = 88.51 β = 90.00
c = 78.04 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2002-01-01
  • Released Date: 2002-07-10
  • Deposition author(s): Chandra, V., Jasti, J., Kaur, P., Betzel, C., Srinivasan, A., Singh, T.P.
  • Previous versions: 1FE7

Revision History

  • 2011-11-16
    Type: Atom occupancy | Details: Atom occupancy
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4