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Structure of Bifidobacterium dentium beta-glucuronidase complexed with C6-hexyl uronic isofagomine
Analyse Structure of Bifidobacterium dentium beta-glucuronidase complexed with C6-hexyl… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6LD0
- Type
- protein
- Length
- 2,480 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.901
- Source
- Bifidobacterium dentium (strain ATCC 27534 / DSM 20436 / JCM 1195 / Bd1)
- Molecule
- LacZ1 Beta-galactosidase
- EC
- 3.2.1.23
- UniProt
- D2Q7B1
- Ligands
- E8X
- Pockets
- 20 · best druggability 0.90
Structure
x-ray diffraction · resolution 1.901 · 1 distinct chain · 21% helix, 34% 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, 34% strand | D2Q7B1 |
Ligands and binding sites
- E8X · (2~{S},3~{S},4~{R},5~{R})-2-hexyl-4,5-bis(oxidanyl) piperidine-3-carboxylic acid · ligand · 4 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1186 | 0.90 | 0.92 | 119 | empty |
| 2 | 434 | 0.81 | 0.89 | 58 | empty |
| 3 | 218 | 0.81 | 0.95 | 34 | empty |
| 4 | 211 | 0.81 | 0.95 | 36 | empty |
| 5 | 390 | 0.80 | 0.89 | 46 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2439 Ų buried · 36 hydrogen bonds · protein-protein
- C–D · 2428 Ų buried · 33 hydrogen bonds · protein-protein
- B–C · 2246 Ų buried · 16 hydrogen bonds · protein-protein
- A–D · 2232 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 612 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 6LD0 · Structure of bifidobacterium dentium beta-glucuronidase complexed with C6-hexyl uronic… · 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 6LD0 · PDBe 6LD0 · UniProt D2Q7B1
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