1KVO

HUMAN PHOSPHOLIPASE A2 COMPLEXED WITH A HIGHLY POTENT SUBSTRATE ANOLOGUE

Structural Biology Knowledgebase: 1KVO SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.273
  • R-Value Work: 0.201

Literature

Macromolecules
Sequence Display for 1KVO

Classification: HYDROLASE

Total Structure Weight: 87173.50

Macromolecule Entities
Molecule Chains Length Organism Details
HUMAN PHOSPHOLIPASE A2 A, B, C..., D, E, FA, B, C, D, E, F 124 Homo sapiens EC#: 3.1.1.4 IUBMB
Gene Name(s): PLA2G2A Gene View PLA2B PLA2L RASF-A
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A, B, C, D, E, F 4-(S)-[(1-OXO-7-PHENYLHEPTYL)AMINO]-5-[4- (PHENYLMETHYL)PHENYLTHIO]PENTANOIC ACID
C31 H37 N O3 S
BLFSPSZATDQQMK-NDEPHWFRSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CA
Query on CA

A, B, C, D, E, F CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
OAP IC50: 21 nM (100) BindingDB

IC50: 13 nM  BindingMOAD
IC50: 13 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.273
  • R-Value Work: 0.201
  • Space Group: P 1 21 1

Unit Cell:

Length (Å) Angle (°)
a = 64.62 α = 90.00
b = 114.44 β = 119.90
c = 64.71 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 1996-07-29
  • Released Date: 1997-07-07
  • Deposition author(s): Cha, S.-S., Abdel-Meguid, S.S., Oh, B.-H.

Revision History

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