Research workbench
Crystal structure of barley limit dextrinase in complex with a branched thio-linked hexasaccharide
Analyse Crystal structure of barley limit dextrinase in complex with a branched… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4J3V
- Type
- protein
- Length
- 872 residues
- Chains
- 1
- 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
- 6 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 32% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Limit dextrinase (EC 3.2.1.41) | protein | 872 | 32% helix, 23% strand | Q9FYY0 |
Ligands and binding sites
- SGD · 6-thio-alpha-D-glucopyranose · ligand · chains A
- GLC · alpha-D-glucopyranose · sugar · 9 copies · chains A
- CA · Calcium ion · metal · chains A
- IOD · Iodide ion · ion · 9 copies · chains A
- CL · Chloride ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 142 | 0.72 | 0.91 | 34 | IOD |
| 2 | 446 | 0.69 | 0.81 | 54 | GLC, SGD |
| 3 | 135 | 0.62 | 0.86 | 29 | IOD |
| 4 | 201 | 0.52 | 0.77 | 26 | empty |
| 5 | 139 | 0.50 | 0.79 | 32 | empty |
Compared structures
- 4J3V · Crystal structure of barley limit dextrinase in complex with a branched thio-linked… · 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 Q9FYY0
- Elsewhere: RCSB PDB 4J3V · PDBe 4J3V · UniProt Q9FYY0
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