MolNFT v1 · #115612 · protein
Uninhibited mouse cyclooxygenase-2 (prostaglandin synthase-2)
5COX: “Uninhibited mouse cyclooxygenase-2 (prostaglandin synthase-2)”. X-ray diffraction, 2 ligands (HEM, NAG), 20 pockets (best druggability 0.82). MolNFT v1 #115612 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5COX
- Type
- protein
- Length
- 2,208 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cyclooxygenase-2
- EC
- 1.14.99.1
- UniProt
- Q05769
- Ligands
- HEM, NAG
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 47% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Cyclooxygenase-2 (EC 1.14.99.1) | protein | 552 | 47% helix, 7% strand | Q05769 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B, C, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 12 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 947 | 0.82 | 0.83 | 86 | empty |
| 2 | 804 | 0.81 | 0.84 | 82 | empty |
| 3 | 908 | 0.81 | 0.83 | 81 | empty |
| 4 | 329 | 0.80 | 0.90 | 45 | empty |
| 5 | 835 | 0.80 | 0.83 | 70 | empty |
Interfaces
4 interfaces between chains.
- A–B · 2486 Ų buried · 48 hydrogen bonds · protein-protein
- C–D · 2476 Ų buried · 48 hydrogen bonds · protein-protein
- A–D · 378 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 29 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 disulfide, 12 glycan (disulfide, N-glycosylation).
Compared structures
- 5COX · Uninhibited mouse cyclooxygenase-2 (prostaglandin synthase-2) · 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 0.99
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 5COX · PDBe 5COX · UniProt Q05769
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