MolNFT v1 · #138195 · protein
COX-1:MOFEZOLAC complex structure
5WBE · Prostaglandin G/H synthase 1: “COX-1:MOFEZOLAC complex structure”. X-ray diffraction, 4 ligands (HEM, 63X, NAG), 5 pockets (best druggability 0.83). MolNFT v1 #138195 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5WBE
- 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, 63X, NAG, MAN
- Pockets
- 5 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 44% 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 | 44% helix, 9% strand | P05979 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- 63X · Mofezolac · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 12 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · 6 copies · chains B, A
- BOG · octyl beta-D-glucopyranoside · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1128 | 0.83 | 0.84 | 116 | BOG, 63X |
| 2 | 1084 | 0.83 | 0.84 | 114 | 63X, BOG |
| 3 | 597 | 0.78 | 0.84 | 80 | empty |
| 4 | 451 | 0.68 | 0.79 | 39 | HEM |
| 5 | 475 | 0.68 | 0.78 | 39 | HEM |
Interfaces
1 interface between chains.
- A–B · 2673 Ų buried · 32 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide, 6 glycan (disulfide, N-glycosylation).
Compared structures
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 5WBE · PDBe 5WBE · UniProt P05979
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