MolNFT v1 · #72447 · protein
Crystal structure of cyclooxygenase-1 in complex with nimesulide
3N8X · Prostaglandin G/H synthase 1: “Crystal structure of cyclooxygenase-1 in complex with nimesulide”. X-ray diffraction, 4 ligands (HEM, NIM, NAG), 8 pockets (best druggability 0.81). MolNFT v1 #72447 on GenesisL1: 3D structure, binding…
- PDB
- 3N8X
- Type
- protein
- Length
- 1,106 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Prostaglandin G/H synthase 1
- EC
- 1.14.99.1
- UniProt
- P05979
- Ligands
- HEM, NIM, NAG, BMA
- Pockets
- 8 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Prostaglandin G/H synthase 1 (EC 1.14.99.1) | protein | 553 | 45% helix, 9% strand | P05979 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- NIM · 4-nitro-2-phenoxymethanesulfonanilide · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 10 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 3 copies · chains B
- BOG · octyl beta-D-glucopyranoside · additive · 2 copies · 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 | 1169 | 0.81 | 0.82 | 108 | NIM |
| 2 | 1168 | 0.79 | 0.80 | 99 | BOG |
| 3 | 133 | 0.78 | 0.95 | 23 | NIM |
| 4 | 567 | 0.76 | 0.83 | 64 | empty |
| 5 | 480 | 0.70 | 0.80 | 43 | HEM |
Interfaces
1 interface between chains.
- A–B · 2607 Ų buried · 30 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide, 6 glycan (disulfide, N-glycosylation).
Compared structures
- 3N8X · Crystal Structure of Cyclooxygenase-1 in Complex with Nimesulide · the same entry in another collection · chain A against A, TM-score 1.00
- P05979 · AlphaFold monomer V2.0 prediction for prostaglandin G/H synthase 1 (P05979) · 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 P05979
- Elsewhere: RCSB PDB 3N8X · PDBe 3N8X · UniProt P05979
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