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Crystal structure of mutant (D286N) GH3 beta-glucosidase from bacteroides thetaiotaomicron in complex with sophorotriose
Analyse Crystal structure of mutant (D286N) GH3 beta-glucosidase from bacteroides… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5XXO
- Type
- protein
- Length
- 1,477 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Periplasmic beta-glucosidase
- UniProt
- Q8A1U1
- Ligands
- BGC, MG
- Pockets
- 17 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Periplasmic beta-glucosidase | protein | 745 | 34% helix, 20% strand | Q8A1U1 |
| B | Periplasmic beta-glucosidase | protein | 732 | 34% helix, 20% strand | Q8A1U1 |
Ligands and binding sites
- BGC · beta-D-glucopyranose · sugar · 4 copies · chains B, A
- MG · Magnesium ion · metal · 2 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · chains A
- PG4 · Tetraethylene glycol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 290 | 0.85 | 0.96 | 36 | empty |
| 2 | 300 | 0.71 | 0.84 | 48 | empty |
| 3 | 306 | 0.68 | 0.83 | 44 | empty |
| 4 | 288 | 0.64 | 0.81 | 39 | empty |
| 5 | 285 | 0.63 | 0.80 | 37 | empty |
Interfaces
1 interface between chains.
- A–B · 3575 Ų buried · 96 hydrogen bonds · protein-protein
Compared structures
- 5XXO · Crystal structure of mutant (D286N) GH3 beta-glucosidase from Bacteroides… · 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 Q8A1U1
- Elsewhere: RCSB PDB 5XXO · PDBe 5XXO · UniProt Q8A1U1
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