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X-ray crystal structure of 1-arachidonoyl glycerol bound to the cyclooxygenase channel of R513H murine COX-2
Analyse X-ray crystal structure of 1-arachidonoyl glycerol bound to the cyclooxygenase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3OLU
- Type
- protein
- Length
- 1,102 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Prostaglandin G/H synthase 2
- EC
- 1.14.99.1
- UniProt
- Q05769
- Ligands
- 1AG, COH, NAG, MAN
- Pockets
- 11 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 47% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Prostaglandin G/H synthase 2 (EC 1.14.99.1) | protein | 551 | 47% helix, 9% strand | Q05769 |
Ligands and binding sites
- 1AG · (2S)-2,3-dihydroxypropyl (5Z,8Z,11Z,14Z)-icosa-5,8,11, 14-tetraenoate · ligand · 2 copies · chains A, B
- COH · Protoporphyrin IX containing co · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 10 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · 2 copies
- EDO · 1,2-ethanediol · additive · 14 copies · chains A, B
- BOG · octyl beta-D-glucopyranoside · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 851 | 0.83 | 0.85 | 96 | empty |
| 2 | 281 | 0.81 | 0.92 | 48 | EDO, 1AG |
| 3 | 684 | 0.80 | 0.84 | 68 | EDO |
| 4 | 199 | 0.78 | 0.92 | 42 | EDO, 1AG |
| 5 | 414 | 0.77 | 0.86 | 60 | empty |
Interfaces
1 interface between chains.
- A–B · 2655 Ų buried · 45 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide, 6 glycan (disulfide, N-glycosylation).
Compared structures
- 3OLU · X-ray crystal structure of 1-arachidonoyl glycerol bound to the cyclooxygenase channel of… · the same entry in another collection · chain A against A, TM-score 1.00
- Q05769 · AlphaFold monomer V2.0 prediction for prostaglandin G/H synthase 2 (Q05769) · a predicted model of the same protein · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q05769
- Elsewhere: RCSB PDB 3OLU · PDBe 3OLU · UniProt Q05769
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