MolNFT v1 · #118418 · protein
The crystal structure of aspirin acetylated human cyclooxygenase-2
5F19 · Prostaglandin G/H synthase 2: “The crystal structure of aspirin acetylated human cyclooxygenase-2”. X-ray diffraction, 4 ligands (AKR, COH, NAG), 8 pockets (best druggability 0.84). MolNFT v1 #118418 on GenesisL1: 3D structure…
- PDB
- 5F19
- Type
- protein
- Length
- 1,104 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
- P35354
- Ligands
- AKR, COH, NAG, MAN
- Pockets
- 8 · best druggability 0.84
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 | 552 | 47% helix, 9% strand | P35354 |
Ligands and binding sites
- AKR · Acrylic acid · ligand · 4 copies · chains A, B
- COH · Protoporphyrin IX containing co · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 9 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · 2 copies
- EDO · 1,2-ethanediol · additive · 15 copies · chains A, B
- BOG · octyl beta-D-glucopyranoside · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1166 | 0.84 | 0.85 | 126 | EDO |
| 2 | 790 | 0.83 | 0.86 | 89 | EDO |
| 3 | 864 | 0.81 | 0.84 | 89 | EDO |
| 4 | 405 | 0.78 | 0.87 | 45 | EDO |
| 5 | 447 | 0.72 | 0.81 | 43 | COH, AKR |
Interfaces
1 interface between chains.
- A–B · 2521 Ų buried · 39 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide, 6 glycan, 2 covalent, 2 modified (disulfide, N-glycosylation, covalent ligand, nonstandard).
Compared structures
- 5F19 · The Crystal Structure of Aspirin Acetylated Human Cyclooxygenase-2 · the same entry in another collection · chain A against A, TM-score 1.00
- P35354 · AlphaFold monomer V2.0 prediction for prostaglandin G/H synthase 2 (P35354) · 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 P35354
- Elsewhere: RCSB PDB 5F19 · PDBe 5F19 · UniProt P35354
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