3RDE

Crystal structure of the catalytic domain of porcine leukocyte 12-lipoxygenase

Structural Biology Knowledgebase: 3RDE SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free: 0.214
  • R-Value Work: 0.172

Literature

Macromolecules
Sequence Display for 3RDE

Classification: OXIDOREDUCTASE / OXIDOREDUCTASE inhibitor

Total Structure Weight: 260803.23

Macromolecule Entities
Molecule Chains Length Organism Details
Arachidonate 12-lipoxygenase, 12S-type A, B, C, D 573 Sus scrofa EC#: 1.13.11.31 IUBMB
Fragment: unp residues 112-663
Mutation: C210S, Q218R, C292S
Gene Name(s): ALOX15 Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A, B, C, D 3-{4-[(tridec-2-yn-1-yloxy)methyl]phenyl}propanoic acid
C23 H34 O3
RYRHYCDBTFUGMI-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
FE2
Query on FE2

A, B, C, D FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
K
Query on K

A, D POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
OYP IC50: 35 nM (99) BindingDB

N/A in BindingMoad
IC50: 35 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free: 0.214
  • R-Value Work: 0.172
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 83.45 α = 90.00
b = 181.54 β = 92.86
c = 91.61 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2011-04-01
  • Released Date: 2012-04-18
  • Deposition author(s): Funk, M.O., Xu, S., Marnett, L.J., Mueser, T.C.

Revision History

  • 2012-09-26
    Type: Citation | Details: Citation update
  • 2012-08-01
    Type: Citation | Details: Citation update
  • 2012-06-20
    Type: Citation | Details: --