Research workbench
Bombyx mori GH13 sucrose hydrolase mutant E322Q covalent intermediate complexed with fructose
Analyse Bombyx mori GH13 sucrose hydrolase mutant E322Q covalent intermediate complexed… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6LGI
- 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
- BDF, BGC, FRU, MG, CA
- Pockets
- 7 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 30% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Sucrose hydrolase | protein | 570 | 30% helix, 19% strand | A0A077JI83 |
Ligands and binding sites
- BDF · beta-D-fructopyranose · ligand · 2 copies · chains A, B
- BGC · beta-D-glucopyranose · sugar · 2 copies · chains A, B
- FRU · beta-D-fructofuranose · sugar · 2 copies · chains A, B
- MG · Magnesium ion · metal · 5 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, B
- ACT · Acetate ion · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 977 | 0.78 | 0.80 | 76 | MG |
| 2 | 324 | 0.64 | 0.80 | 39 | MG, BGC, FRU |
| 3 | 277 | 0.62 | 0.80 | 30 | MG, BGC, FRU |
| 4 | 322 | 0.53 | 0.74 | 39 | empty |
| 5 | 282 | 0.52 | 0.74 | 44 | empty |
Interfaces
1 interface between chains.
- A–B · 1203 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 glycan (glycosylation).
Compared structures
- 6LGI · Bombyx mori GH13 sucrose hydrolase mutant E322Q covalent intermediate complexed with… · 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 6LGI · PDBe 6LGI · UniProt A0A077JI83
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