MolNFT v1 · #155723 · protein
Bombyx mori GH13 sucrose hydrolase mutant D247N complexed with sucrose
6LGF: “Bombyx mori GH13 sucrose hydrolase mutant D247N complexed with sucrose”. X-ray diffraction, 4 ligands (GLC, FRU, MG), 9 pockets (best druggability 0.74). MolNFT v1 #155723 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 6LGF
- Type
- protein
- Length
- 1,134 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sucrose hydrolase
- UniProt
- A0A077JI83
- Ligands
- GLC, FRU, MG, CA
- Pockets
- 9 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 30% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sucrose hydrolase | protein | 565 | 30% helix, 20% strand | A0A077JI83 |
| B | Sucrose hydrolase | protein | 569 | 29% helix, 19% strand | A0A077JI83 |
Ligands and binding sites
- GLC · alpha-D-glucopyranose · sugar · 2 copies · chains A, B
- FRU · beta-D-fructofuranose · sugar · 2 copies · chains A, B
- MG · Magnesium ion · metal · 4 copies · chains A, B
- CA · Calcium ion · metal · 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 809 | 0.74 | 0.79 | 70 | empty |
| 2 | 325 | 0.64 | 0.80 | 39 | GLC, FRU, MG |
| 3 | 287 | 0.61 | 0.79 | 35 | GLC, FRU, MG |
| 4 | 273 | 0.55 | 0.76 | 36 | empty |
| 5 | 321 | 0.54 | 0.75 | 43 | empty |
Interfaces
1 interface between chains.
- A–B · 1264 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 6LGF · Bombyx mori GH13 sucrose hydrolase mutant D247N complexed with sucrose · 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 A0A077JI83
- Elsewhere: RCSB PDB 6LGF · PDBe 6LGF · UniProt A0A077JI83
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