MolNFT v1 · #155620 · protein
Structure of bifidobacterium dentium beta-glucuronidase complexed with C6-nonyl uronic isofagomine
6LDC · LACZ1 beta-galactosidase: “Structure of bifidobacterium dentium beta-glucuronidase complexed with C6-nonyl uronic isofagomine”. X-ray diffraction, 1 ligand (E9O), 20 pockets (best druggability 0.91). MolNFT v1 #155620 on GenesisL1…
- PDB
- 6LDC
- Type
- protein
- Length
- 2,468 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
- E9O
- Pockets
- 20 · best druggability 0.91
Structure
x-ray diffraction · 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 | 617 | 21% helix, 34% strand | D2Q7B1 |
Ligands and binding sites
- E9O · (2~{S},3~{S},4~{R},5~{R})-2-nonyl-4,5-bis(oxidanyl) piperidine-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 | 754 | 0.91 | 0.96 | 106 | empty |
| 2 | 601 | 0.84 | 0.89 | 76 | empty |
| 3 | 518 | 0.83 | 0.89 | 71 | empty |
| 4 | 224 | 0.82 | 0.96 | 36 | empty |
| 5 | 193 | 0.81 | 0.96 | 35 | empty |
Interfaces
6 interfaces between chains.
- A–C · 2488 Ų buried · 34 hydrogen bonds · protein-protein
- B–D · 2413 Ų buried · 34 hydrogen bonds · protein-protein
- C–D · 2094 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 2062 Ų buried · 15 hydrogen bonds · protein-protein
- A–D · 618 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 6LDC · Structure of Bifidobacterium dentium beta-glucuronidase complexed with C6-nonyl 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 6LDC · PDBe 6LDC · UniProt D2Q7B1
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