MolNFT v1 · #140028 · protein
Crystal structure of GH3 beta-glucosidase from bacteroides thetaiotaomicron in complex with gluconolactone
5XXM · Periplasmic beta-glucosidase: “Crystal structure of GH3 beta-glucosidase from bacteroides thetaiotaomicron in complex with gluconolactone”. X-ray diffraction, 2 ligands (LGC, MG), 14 pockets (best druggability 0.86). MolNFT v1…
- PDB
- 5XXM
- Type
- protein
- Length
- 1,493 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Periplasmic beta-glucosidase
- UniProt
- Q8A1U1
- Ligands
- LGC, MG
- Pockets
- 14 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Periplasmic beta-glucosidase | protein | 749 | 34% helix, 20% strand | Q8A1U1 |
| B | Periplasmic beta-glucosidase | protein | 744 | 34% helix, 20% strand | Q8A1U1 |
Ligands and binding sites
- LGC · D-glucono-1,5-lactone · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- PG4 · Tetraethylene glycol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 302 | 0.86 | 0.97 | 36 | empty |
| 2 | 301 | 0.73 | 0.86 | 45 | empty |
| 3 | 302 | 0.71 | 0.84 | 49 | empty |
| 4 | 316 | 0.67 | 0.82 | 42 | empty |
| 5 | 324 | 0.64 | 0.80 | 40 | empty |
Interfaces
1 interface between chains.
- A–B · 3696 Ų buried · 97 hydrogen bonds · protein-protein
Compared structures
- 5XXM · Crystal structure of GH3 beta-glucosidase from Bacteroides thetaiotaomicron in complex… · 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 5XXM · PDBe 5XXM · UniProt Q8A1U1
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