Research workbench
Crystal structure of AGD31B, alpha-transglucosylase, complexed with acarbose
Analyse Crystal structure of AGD31B, alpha-transglucosylase, complexed with acarbose in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4B9Z
- 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
- AC1, OXL, GLC, SO4
- Pockets
- 7 · best druggability 0.56
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
- AC1 · 4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-alpha-D-glucopyranose · ligand · chains A
- OXL · Oxalate ion · ligand · chains A
- GLC · alpha-D-glucopyranose · sugar · 2 copies · chains A
- SO4 · Sulfate ion · ion · 5 copies · chains A
- EDO · 1,2-ethanediol · additive · 15 copies · chains A
- PEG · Di(hydroxyethyl)ether · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 111 | 0.56 | 0.84 | 24 | AC1 |
| 2 | 219 | 0.54 | 0.78 | 32 | EDO |
| 3 | 187 | 0.52 | 0.78 | 31 | empty |
| 4 | 51 | 0.40 | 0.82 | 19 | empty |
| 5 | 86 | 0.39 | 0.77 | 18 | EDO |
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 4B9Z · Crystal Structure of Agd31B, alpha-transglucosylase, complexed with Acarbose · 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 4B9Z · PDBe 4B9Z · UniProt B3PEE6
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