MolNFT v1 · #54940 · protein
Barley limit dextrinase in complex with beta-cyclodextrin
2Y4S: “Barley limit dextrinase in complex with beta-cyclodextrin”. X-ray diffraction, 3 ligands (GLC, CA, IOD), 7 pockets (best druggability 0.69). MolNFT v1 #54940 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2Y4S
- Type
- protein
- Length
- 863 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Limit dextrinase
- EC
- 3.2.1.41
- UniProt
- O48541
- Ligands
- GLC, CA, IOD
- Pockets
- 7 · best druggability 0.69
Structure
x-ray diffraction · 1 distinct chain · 31% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Limit dextrinase (EC 3.2.1.41) | protein | 863 | 31% helix, 22% strand | O48541 |
Ligands and binding sites
- GLC · alpha-D-glucopyranose · sugar · 7 copies · chains A
- CA · Calcium ion · metal · 2 copies · chains A
- IOD · Iodide ion · ion · 5 copies · chains A
- GOL · Glycerol · additive · 7 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 123 | 0.69 | 0.91 | 22 | empty |
| 2 | 205 | 0.67 | 0.85 | 36 | GOL |
| 3 | 473 | 0.65 | 0.77 | 51 | GLC, GOL |
| 4 | 94 | 0.56 | 0.85 | 23 | empty |
| 5 | 191 | 0.52 | 0.78 | 25 | empty |
Compared structures
- 2Y4S · Barley limit dextrinase in complex with beta-cyclodextrin · 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 O48541
- Elsewhere: RCSB PDB 2Y4S · PDBe 2Y4S · UniProt O48541
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.