MolNFT v1 · #178722 · protein
Eubacterium rectale AMY13B (EUR_01860)
7JJN · Glycosidases: “Eubacterium rectale AMY13B (EUR_01860)”. X-ray diffraction, 4 ligands (GLC, BGC, CA), 9 pockets (best druggability 0.68). MolNFT v1 #178722 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7JJN
- Type
- protein
- Length
- 1,023 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycosidases
- EC
- 3.2.1.1
- UniProt
- D6E1Y4
- Ligands
- GLC, BGC, CA, SO4
- Pockets
- 9 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycosidases (EC 3.2.1.1) | protein | 514 | 34% helix, 18% strand | D6E1Y4 |
| B | Glycosidases (EC 3.2.1.1) | protein | 509 | 34% helix, 17% strand | D6E1Y4 |
Ligands and binding sites
- GLC · alpha-D-glucopyranose · sugar · 4 copies · chains A, B
- BGC · beta-D-glucopyranose · sugar · 2 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 556 | 0.68 | 0.78 | 59 | empty |
| 2 | 683 | 0.67 | 0.76 | 55 | EDO, SO4 |
| 3 | 134 | 0.52 | 0.80 | 21 | BGC, GLC |
| 4 | 122 | 0.50 | 0.80 | 19 | BGC, GLC |
| 5 | 88 | 0.47 | 0.81 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 638 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 7JJN · Eubacterium rectale Amy13B (EUR_01860) · the same entry in another collection · 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 D6E1Y4
- Elsewhere: RCSB PDB 7JJN · PDBe 7JJN · UniProt D6E1Y4
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.