Research workbench
2-deoxy-galactose reaction intermediate of a truncated beta- galactosidase III from bifidobacterium bifidum
Analyse 2-deoxy-galactose reaction intermediate of a truncated beta- galactosidase III… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6QUD
- Type
- protein
- Length
- 837 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-galactosidase
- EC
- 3.2.1.23
- UniProt
- Q9F4D5
- Ligands
- 2DG, CA
- Pockets
- 12 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 14% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-galactosidase (EC 3.2.1.23) | protein | 837 | 14% helix, 39% strand | Q9F4D5 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1166 | 0.75 | 0.78 | 108 | empty |
| 2 | 455 | 0.67 | 0.79 | 46 | empty |
| 3 | 124 | 0.63 | 0.87 | 20 | empty |
| 4 | 336 | 0.60 | 0.77 | 42 | empty |
| 5 | 125 | 0.48 | 0.79 | 28 | empty |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 6QUD · 2-deoxy-galactose reaction intermediate of a Truncated beta-galactosidase III from… · 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 Q9F4D5
- Elsewhere: RCSB PDB 6QUD · PDBe 6QUD · UniProt Q9F4D5
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