MolNFT v1 · #95889 · protein
Crystal structure of barley limit dextrinase in complex with maltosyl- S-betacyclodextrin
4J3U: “Crystal structure of barley limit dextrinase in complex with maltosyl- S-betacyclodextrin”. X-ray diffraction, 5 ligands (SGD, GLC, CA), 14 pockets (best druggability 0.78). MolNFT v1 #95889 on GenesisL1: 3D structure, binding sites…
- PDB
- 4J3U
- Type
- protein
- Length
- 1,734 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Limit dextrinase
- EC
- 3.2.1.41
- UniProt
- Q9FYY0
- Ligands
- SGD, GLC, CA, IOD, CL
- Pockets
- 14 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Limit dextrinase (EC 3.2.1.41) | protein | 870 | 32% helix, 23% strand | Q9FYY0 |
| B | Limit dextrinase (EC 3.2.1.41) | protein | 864 | 32% helix, 22% strand | Q9FYY0 |
Ligands and binding sites
- SGD · 6-thio-alpha-D-glucopyranose · ligand · 2 copies · chains A, B
- GLC · alpha-D-glucopyranose · sugar · 16 copies · chains A, B
- CA · Calcium ion · metal · 4 copies · chains A, B
- IOD · Iodide ion · ion · 32 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1075 | 0.78 | 0.80 | 103 | SGD, GLC |
| 2 | 585 | 0.72 | 0.80 | 70 | SGD, GLC |
| 3 | 121 | 0.65 | 0.88 | 32 | empty |
| 4 | 143 | 0.63 | 0.85 | 30 | empty |
| 5 | 132 | 0.63 | 0.86 | 30 | IOD |
Interfaces
1 interface between chains.
- A–B · 280 Ų buried · 5 hydrogen bonds · protein-protein
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 Q9FYY0
- Elsewhere: RCSB PDB 4J3U · PDBe 4J3U · UniProt Q9FYY0
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