MolNFT v1 · #155725 · protein
Bombyx mori GH13 sucrose hydrolase mutant E322Q covalent intermediate
6LGH: “Bombyx mori GH13 sucrose hydrolase mutant E322Q covalent intermediate”. X-ray diffraction, 3 ligands (BGC, MG, CA), 11 pockets (best druggability 0.71). MolNFT v1 #155725 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6LGH
- Type
- protein
- Length
- 1,133 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sucrose hydrolase
- UniProt
- A0A077JI83
- Ligands
- BGC, MG, CA
- Pockets
- 11 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 30% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sucrose hydrolase | protein | 565 | 30% helix, 20% strand | A0A077JI83 |
| B | Sucrose hydrolase | protein | 568 | 29% helix, 20% strand | A0A077JI83 |
Ligands and binding sites
- BGC · beta-D-glucopyranose · sugar · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 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
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 571 | 0.71 | 0.80 | 43 | empty |
| 2 | 296 | 0.62 | 0.80 | 44 | BGC |
| 3 | 317 | 0.62 | 0.79 | 42 | BGC |
| 4 | 297 | 0.54 | 0.76 | 44 | empty |
| 5 | 254 | 0.54 | 0.76 | 29 | empty |
Interfaces
1 interface between chains.
- A–B · 1257 Ų buried · 22 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 glycan (glycosylation).
Compared structures
- 6LGH · Bombyx mori GH13 sucrose hydrolase mutant E322Q covalent intermediate · 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 6LGH · PDBe 6LGH · UniProt A0A077JI83
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