MolNFT v1 · #155720 · protein
Bombyx mori GH13 sucrose hydrolase complexed with 1-deoxynojirimycin
6LGC: “Bombyx mori GH13 sucrose hydrolase complexed with 1-deoxynojirimycin”. X-ray diffraction, 3 ligands (NOJ, MG, CA), 9 pockets (best druggability 0.78). MolNFT v1 #155720 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6LGC
- Type
- protein
- Length
- 1,140 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sucrose hydrolase
- UniProt
- A0A077JI83
- Ligands
- NOJ, MG, CA
- Pockets
- 9 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 29% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Sucrose hydrolase | protein | 570 | 29% helix, 19% strand | A0A077JI83 |
Ligands and binding sites
- NOJ · 1-deoxynojirimycin · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 3 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, B
- GOL · Glycerol · additive · 4 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 | 969 | 0.78 | 0.80 | 78 | MG |
| 2 | 360 | 0.65 | 0.80 | 43 | NOJ, GOL |
| 3 | 314 | 0.64 | 0.80 | 42 | NOJ, GOL |
| 4 | 300 | 0.53 | 0.74 | 39 | empty |
| 5 | 324 | 0.53 | 0.74 | 45 | empty |
Interfaces
1 interface between chains.
- A–B · 1124 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 6LGC · Bombyx mori GH13 sucrose hydrolase complexed with 1-deoxynojirimycin · 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 6LGC · PDBe 6LGC · UniProt A0A077JI83
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