MolNFT v1 · #126621 · protein
Crystal structure of alpha-L-arabinofuranosidase from lactobacillus brevis
5M8B · Alpha-L-arabinofuranosidase II: “Crystal structure of alpha-L-arabinofuranosidase from lactobacillus brevis”. X-ray diffraction, 1 ligand (MG), 8 pockets (best druggability 0.71). MolNFT v1 #126621 on GenesisL1: 3D structure…
- PDB
- 5M8B
- Type
- protein
- Length
- 650 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-L-arabinofuranosidase II
- EC
- 3.2.1.55
- UniProt
- A0A0D0G8J8
- Ligands
- MG
- Pockets
- 8 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 7% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Alpha-L-arabinofuranosidase II (EC 3.2.1.55) | protein | 325 | 7% helix, 46% strand | A0A0D0G8J8 |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains A, B
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 4 copies · chains A, B
- PGE · Triethylene glycol · additive · 2 copies · chains A
- 1PE · Pentaethylene glycol · additive · chains A, B
- PG4 · Tetraethylene glycol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 518 | 0.71 | 0.80 | 64 | empty |
| 2 | 354 | 0.68 | 0.81 | 35 | TRS, PGE |
| 3 | 124 | 0.68 | 0.90 | 26 | TRS, PG4 |
| 4 | 322 | 0.61 | 0.78 | 29 | empty |
| 5 | 282 | 0.57 | 0.77 | 27 | TRS |
Interfaces
1 interface between chains.
- A–B · 1424 Ų buried · 25 hydrogen bonds · protein-protein
Compared structures
- 5M8B · Crystal structure of alpha-L-arabinofuranosidase from Lactobacillus brevis · 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 A0A0D0G8J8
- Elsewhere: RCSB PDB 5M8B · PDBe 5M8B · UniProt A0A0D0G8J8
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.