MolNFT v1 · #74066 · protein
X-ray crystal structure of arachidonic acid bound to the cyclooxygenase channel of R513H murine COX-2
3OLT · Prostaglandin G/H synthase 2: “X-ray crystal structure of arachidonic acid bound to the cyclooxygenase channel of R513H murine COX-2”. X-ray diffraction, 4 ligands (ACD, COH, NAG), 10 pockets (best druggability 0.82). MolNFT v1…
- PDB
- 3OLT
- 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
- ACD, COH, NAG, MAN
- Pockets
- 10 · best druggability 0.82
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
- ACD · Arachidonic acid · 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
10 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 277 | 0.82 | 0.93 | 44 | EDO, ACD |
| 2 | 482 | 0.82 | 0.88 | 64 | EDO, ACD |
| 3 | 1156 | 0.79 | 0.81 | 106 | empty |
| 4 | 654 | 0.79 | 0.84 | 59 | EDO |
| 5 | 404 | 0.77 | 0.86 | 59 | empty |
Interfaces
1 interface between chains.
- A–B · 2637 Ų buried · 45 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide, 6 glycan (disulfide, N-glycosylation).
Compared structures
- 3OLT · X-ray crystal structure of arachidonic acid bound to the cyclooxygenase channel of R513H… · the same entry in another collection · chain B against B, 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 3OLT · PDBe 3OLT · UniProt Q05769
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