MolNFT v1 · #128407 · protein
Crystal structure of CJAGD31B (alpha-transglucosylase from glycoside hydrolase family 31) in complex with alpha cyclophellitol cyclosulfate probe ME647
5NPB · Oligosaccharide 4-alpha-D-glucosyltransferase: “Crystal structure of CJAGD31B (alpha-transglucosylase from glycoside hydrolase family 31) in complex with…”. X-ray diffraction, 3 ligands (93Z, OXL, SO4), 6 pockets (best druggability…
- PDB
- 5NPB
- Type
- protein
- Length
- 780 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
- 93Z, OXL, SO4
- Pockets
- 6 · 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 | 780 | 21% helix, 33% strand | B3PEE6 |
Ligands and binding sites
- 93Z · [(1~{S},2~{R},3~{R},4~{S},5~{R})-2-(hydroxymethyl)-3,4, 5,6-tetrakis(oxidanyl)cyclohexyl] hydrogen sulfate · ligand · chains A
- OXL · Oxalate ion · ligand · chains A
- SO4 · Sulfate ion · ion · 5 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
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 231 | 0.57 | 0.79 | 34 | empty |
| 2 | 232 | 0.57 | 0.79 | 37 | empty |
| 3 | 160 | 0.57 | 0.81 | 24 | 93Z |
| 4 | 119 | 0.44 | 0.77 | 28 | empty |
| 5 | 111 | 0.38 | 0.74 | 19 | PG4 |
Modifications
Observed in the structure: 1 covalent, 1 disulfide (covalent ligand, disulfide).
Compared structures
- 5NPB · Crystal Structure of cjAgd31B (alpha-transglucosylase from 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 5NPB · PDBe 5NPB · UniProt B3PEE6
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