Research workbench
Crystal structure of AGD31B, alpha-transglucosylase in glycoside hydrolase family 31, in complex with cyclophellitol aziridine probe CF021
Analyse Crystal structure of 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
- 5I24
- Type
- protein
- Length
- 779 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Oligosaccharide 4-alpha-D-glucosyltransferase
- EC
- 2.4.1.161
- UniProt
- B3PEE6
- Ligands
- 66U, SO4
- Pockets
- 7 · best druggability 0.57
Structure
x-ray diffraction · 1 distinct chain · 21% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Oligosaccharide 4-alpha-D-glucosyltransferase (EC 2.4.1.161) | protein | 779 | 21% helix, 33% strand | B3PEE6 |
Ligands and binding sites
- 66U · (1R,2S,3S,4R,5S,6R)-5-amino-6-(hydroxymethyl)cyclohexane-1,2,3,4-tetrol · ligand · chains A
- SO4 · Sulfate ion · ion · 5 copies · chains A
- EDO · 1,2-ethanediol · additive · 3 copies · chains A
- PG4 · Tetraethylene glycol · additive · chains A
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · 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 | 237 | 0.57 | 0.79 | 36 | empty |
| 2 | 225 | 0.55 | 0.78 | 36 | empty |
| 3 | 157 | 0.55 | 0.80 | 25 | 66U |
| 4 | 98 | 0.41 | 0.77 | 24 | empty |
| 5 | 107 | 0.35 | 0.73 | 22 | PG4, EDO |
Modifications
Observed in the structure: 1 covalent, 1 disulfide (covalent ligand, disulfide).
Compared structures
- 5I24 · Crystal Structure of Agd31B, alpha-transglucosylase in Glycoside Hydrolase Family 31, in… · 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 5I24 · PDBe 5I24 · UniProt B3PEE6
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