MolNFT v1 · #41128 · protein
Structure of a beta-mannosidase from bacteroides thetaiotaomicron
2JE8: “Structure of a beta-mannosidase from bacteroides thetaiotaomicron”. X-ray diffraction, 1 ligand (CL), 13 pockets (best druggability 0.79). MolNFT v1 #41128 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2JE8
- Type
- protein
- Length
- 1,678 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-mannosidase
- EC
- 3.2.1.25
- UniProt
- Q8AAK6
- Ligands
- CL
- Pockets
- 13 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 23% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-mannosidase (EC 3.2.1.25) | protein | 837 | 24% helix, 36% strand | Q8AAK6 |
| B | Beta-mannosidase (EC 3.2.1.25) | protein | 841 | 23% helix, 36% strand | Q8AAK6 |
Ligands and binding sites
- CL · Chloride ion · ion · 4 copies · chains A, B
- GOL · Glycerol · additive · 9 copies · chains A, B
- B3P · 2-[3-(2-hydroxy-1,1-dihydroxymethyl-ethylamino)-propylamino]-2-hydroxymethyl-propane-1,3-diol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 717 | 0.79 | 0.83 | 53 | empty |
| 2 | 597 | 0.77 | 0.83 | 56 | empty |
| 3 | 1075 | 0.75 | 0.78 | 85 | GOL |
| 4 | 848 | 0.70 | 0.76 | 68 | GOL |
| 5 | 639 | 0.67 | 0.76 | 55 | empty |
Interfaces
1 interface between chains.
- A–B · 927 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 2JE8 · Structure of a beta-mannosidase from Bacteroides thetaiotaomicron · 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 Q8AAK6
- Elsewhere: RCSB PDB 2JE8 · PDBe 2JE8 · UniProt Q8AAK6
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