3QH0

X-ray crystal structure of palmitic acid bound to the cyclooxygenase channel of cyclooxygenase-2

Structural Biology Knowledgebase: 3QH0 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.199
  • R-Value Work: 0.159

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3QH0

Classification: OXIDOREDUCTASE

Total Structure Weight: 145420.72

Macromolecule Entities
Molecule Chains Length Organism Details
Prostaglandin G/H synthase 2 A, B 610 Mus musculus EC#: 1.14.99.1 IUBMB
Fragment: UNP Residue 1-608
Mutation: N594A
Gene Name(s): Ptgs2 Cox-2 Cox2 Pghs-b Tis10

Membrane Protein

Source: inferred by homology | Group: MONOTOPIC MEMBRANE PROTEINS

Subgroup Name: Cyclooxygenases

Protein Name: Cyclooxygenase-2


Small Molecules
Ligands 9 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
COH
Query on COH

A, B PROTOPORPHYRIN IX CONTAINING CO
C34 H32 Co N4 O4
AQTFKGDWFRRIHR-CTESUSPADG
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
BOG
Query on BOG

A B-OCTYLGLUCOSIDE
C14 H28 O6
HEGSGKPQLMEBJL-RKQHYHRCSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PLM
Query on PLM

A PALMITIC ACID
C16 H32 O2
IPCSVZSSVZVIGE-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NDG
Query on NDG

B 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
C8 H15 N O6
OVRNDRQMDRJTHS-PVFLNQBWSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
HSQ
Query on HSQ

A 2-(acetylamino)-2-deoxy-alpha-L-idopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-SLBCVNJHSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NAG
Query on NAG

A, B N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MAN
Query on MAN

A ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
AKR
Query on AKR

A ACRYLIC ACID
C3 H4 O2
NIXOWILDQLNWCW-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
EDO
Query on EDO

A, B 1,2-ETHANEDIOL
ETHYLENE GLYCOL (Synonym)
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
PLM IC50: >500000 nM (86) BindingDB

N/A in BindingMoad
N/A in PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.199
  • R-Value Work: 0.159
  • Space Group: I 2 2 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 121.91 α = 90.00
b = 130.89 β = 90.00
c = 179.97 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2011-01-25
  • Released Date: 2011-04-13
  • Deposition author(s): Vecchio, A.J., Malkowski, M.G.

Revision History

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