MolNFT v1 · #146006 · protein
Eubacterium eligens beta-glucuronidase bound to an amoxapine- glucuronide conjugate
6D4O: “Eubacterium eligens beta-glucuronidase bound to an amoxapine- glucuronide conjugate”. X-ray diffraction, 3 ligands (FUV, NA, CL), 4 pockets (best druggability 0.74). MolNFT v1 #146006 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6D4O
- Type
- protein
- Length
- 589 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-glucuronidase
- EC
- 3.2.1.31
- UniProt
- A0A174ZZA3
- Ligands
- FUV, NA, CL
- Pockets
- 4 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 19% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-glucuronidase (EC 3.2.1.31) | protein | 589 | 19% helix, 29% strand | A0A174ZZA3 |
Ligands and binding sites
- FUV · (5aR,9aR)-2-chloro-11-(4-beta-D-glucopyranuronosylpiperazin-1-yl)-5a,6,9,9a-tetrahydrodibenzo[b,f][1,4]oxazepine · ligand · chains A
- NA · Sodium ion · metal · chains A
- CL · Chloride ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 505 | 0.74 | 0.83 | 58 | FUV |
| 2 | 77 | 0.63 | 0.91 | 21 | empty |
| 3 | 58 | 0.36 | 0.79 | 22 | empty |
| 4 | 59 | 0.28 | 0.74 | 13 | empty |
Compared structures
- 6D4O · Eubacterium eligens beta-glucuronidase bound to an amoxapine-glucuronide conjugate · 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 A0A174ZZA3
- Elsewhere: RCSB PDB 6D4O · PDBe 6D4O · UniProt A0A174ZZA3
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