Research workbench
Structure of bifidobacterium dentium beta-glucuronidase complexed with uronic isofagomine
Analyse Structure of bifidobacterium dentium beta-glucuronidase complexed with uronic… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6LDB
- Type
- protein
- Length
- 2,480 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- LACZ1 beta-galactosidase
- EC
- 3.2.1.23
- UniProt
- D2Q7B1
- Ligands
- SJ5
- Pockets
- 20 · best druggability 0.90
Structure
x-ray diffraction · 1 distinct chain · 21% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | LACZ1 beta-galactosidase (EC 3.2.1.23) | protein | 620 | 21% helix, 35% strand | D2Q7B1 |
Ligands and binding sites
- SJ5 · (3S,4R,5R)-4,5-dihydroxypiperidine-3-carboxylic acid · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1174 | 0.90 | 0.93 | 118 | empty |
| 2 | 1170 | 0.86 | 0.87 | 111 | empty |
| 3 | 612 | 0.84 | 0.89 | 86 | empty |
| 4 | 218 | 0.81 | 0.95 | 35 | empty |
| 5 | 448 | 0.81 | 0.89 | 55 | empty |
Interfaces
6 interfaces between chains.
- C–D · 2412 Ų buried · 34 hydrogen bonds · protein-protein
- A–B · 2386 Ų buried · 35 hydrogen bonds · protein-protein
- B–C · 2299 Ų buried · 17 hydrogen bonds · protein-protein
- A–D · 2276 Ų buried · 16 hydrogen bonds · protein-protein
- B–D · 588 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 6LDB · Structure of Bifidobacterium dentium beta-glucuronidase complexed with uronic isofagomine · 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 D2Q7B1
- Elsewhere: RCSB PDB 6LDB · PDBe 6LDB · UniProt D2Q7B1
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