MolNFT v1 · #116781 · protein
1.8 ångström crystal structure of listeria monocytogenes LMO0184 alpha-1,6-glucosidase
5DO8 · LMO0184 protein: “1.8 ångström crystal structure of listeria monocytogenes LMO0184 alpha-1,6-glucosidase”. X-ray diffraction, 2 ligands (BGC, CL), 13 pockets (best druggability 0.84). MolNFT v1 #116781 on GenesisL1: 3D structure…
- PDB
- 5DO8
- Type
- protein
- Length
- 1,656 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- LMO0184 protein
- UniProt
- Q8YAE6
- Ligands
- BGC, CL
- Pockets
- 13 · best druggability 0.84
Structure
x-ray diffraction · 3 distinct chains · 36% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | LMO0184 protein | protein | 553 | 35% helix, 17% strand | Q8YAE6 |
| A | LMO0184 protein | protein | 552 | 36% helix, 17% strand | Q8YAE6 |
| C | LMO0184 protein | protein | 551 | 36% helix, 17% strand | Q8YAE6 |
Ligands and binding sites
- BGC · beta-D-glucopyranose · sugar · 3 copies · chains B, A, C
- CL · Chloride ion · ion · 4 copies · chains B, A, C
- BTB · 2-[bis-(2-hydroxy-ethyl)-amino]-2-hydroxymethyl-propane-1,3-diol · additive · 3 copies · chains B, A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1085 | 0.84 | 0.85 | 118 | BGC, BTB |
| 2 | 908 | 0.78 | 0.80 | 58 | BGC, BTB |
| 3 | 824 | 0.77 | 0.81 | 56 | BGC, BTB |
| 4 | 450 | 0.63 | 0.77 | 45 | empty |
| 5 | 279 | 0.56 | 0.77 | 27 | empty |
Interfaces
2 interfaces between chains.
- B–A · 817 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 352 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 5DO8 · 1.8 Angstrom crystal structure of Listeria monocytogenes Lmo0184 alpha-1,6-glucosidase · the same entry in another collection · chain B against B, 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 Q8YAE6
- Elsewhere: RCSB PDB 5DO8 · PDBe 5DO8 · UniProt Q8YAE6
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