MolNFT v1 · #127781 · protein
Thermotoga maritima family 1 glycoside hydrolase complexed with a cyclophellitol analogue transition state mimic
5N6T · Beta-glucosidase a: “Thermotoga maritima family 1 glycoside hydrolase complexed with a cyclophellitol analogue transition state…”. X-ray diffraction, 2 ligands (8P2, CL), 6 pockets (best druggability 0.73). MolNFT v1 #127781 on…
- PDB
- 5N6T
- Type
- protein
- Length
- 887 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-glucosidase a
- EC
- 3.2.1.21
- UniProt
- Q08638
- Ligands
- 8P2, CL
- Pockets
- 6 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-glucosidase a (EC 3.2.1.21) | protein | 443 | 44% helix, 19% strand | Q08638 |
| B | Beta-glucosidase a (EC 3.2.1.21) | protein | 444 | 44% helix, 18% strand | Q08638 |
Ligands and binding sites
- 8P2 · [(1~{R},2~{R},3~{R},4~{S},5~{R},6~{S})-3,4,5-tris(oxidanyl)-7-oxabicyclo[4.1.0]heptan-2-yl]methanediazonium · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · chains A, B
- EDO · 1,2-ethanediol · additive · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 514 | 0.73 | 0.81 | 47 | EDO, 8P2 |
| 2 | 528 | 0.72 | 0.80 | 53 | EDO, 8P2 |
| 3 | 177 | 0.45 | 0.75 | 24 | CL |
| 4 | 154 | 0.43 | 0.75 | 23 | empty |
| 5 | 53 | 0.35 | 0.78 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 1142 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 5N6T · Thermotoga maritima family 1 glycoside hydrolase complexed with a cyclophellitol analogue… · the same entry in another collection · chain A against A, TM-score 1.00
- Q08638 · AlphaFold monomer V2.0 prediction for beta-glucosidase a (Q08638) · a predicted model of the same protein · chain B 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 Q08638
- Elsewhere: RCSB PDB 5N6T · PDBe 5N6T · UniProt Q08638
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