Research workbench
Crystal structure of apo AGD31B, alpha-transglucosylase in glycoside hydrolase family 31
Analyse Crystal structure of apo AGD31B, alpha-transglucosylase in glycoside hydrolase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4B9Y
- Type
- protein
- Length
- 780 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-glucosidase, putative, ADG31B
- EC
- 3.2.1.20
- UniProt
- B3PEE6
- Ligands
- OXL, SO4
- Pockets
- 5 · best druggability 0.55
Structure
x-ray diffraction · 1 distinct chain · 21% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alpha-glucosidase, putative, ADG31B (EC 3.2.1.20) | protein | 780 | 21% helix, 33% strand | B3PEE6 |
Ligands and binding sites
- OXL · Oxalate ion · ligand · chains A
- SO4 · Sulfate ion · ion · 10 copies · chains A
- EDO · 1,2-ethanediol · additive · 6 copies · chains A
- PG4 · Tetraethylene glycol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 240 | 0.55 | 0.77 | 35 | empty |
| 2 | 114 | 0.55 | 0.83 | 23 | empty |
| 3 | 169 | 0.53 | 0.79 | 31 | empty |
| 4 | 56 | 0.42 | 0.82 | 21 | empty |
| 5 | 96 | 0.36 | 0.74 | 19 | PG4 |
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 4B9Y · Crystal Structure of Apo Agd31B, alpha-transglucosylase in Glycoside Hydrolase Family 31 · the same entry in another collection · chain A against A, TM-score 1.00
- B3PEE6 · AlphaFold monomer V2.0 prediction for oligosaccharide 4-alpha-D- glucosyltransferase… · a predicted model of the same protein · chain A against A, TM-score 0.99
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 B3PEE6
- Elsewhere: RCSB PDB 4B9Y · PDBe 4B9Y · UniProt B3PEE6
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