Research workbench
Beta-glucuronidase from faecalibacterium prausnitzii bound to the inhibitor UNC10201652-glucuronide
Analyse Beta-glucuronidase from faecalibacterium prausnitzii bound to the inhibitor… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7KGY
- Type
- protein
- Length
- 2,367 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-glucuronidase
- EC
- 3.2.1.31
- Ligands
- I9G
- Pockets
- 20 · best druggability 0.71
Structure
x-ray diffraction · 4 distinct chains · 21% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-glucuronidase (EC 3.2.1.31) | protein | 593 | 21% helix, 35% strand | — |
| B | Beta-glucuronidase (EC 3.2.1.31) | protein | 591 | 21% helix, 35% strand | — |
| C | Beta-glucuronidase (EC 3.2.1.31) | protein | 591 | 20% helix, 35% strand | — |
| D | Beta-glucuronidase (EC 3.2.1.31) | protein | 592 | 21% helix, 35% strand | — |
Ligands and binding sites
- I9G · 8-(4-beta-D-glucopyranuronosylpiperazin-1-yl)-5-(morpholin-4-yl)-1,2,3,4-tetrahydro[1,2,3]triazino[4', 5':4,5]thieno[2,3 -c]isoquinoline · ligand · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 3 copies · chains A, B, 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, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 59 | 0.71 | 0.97 | 20 | GOL |
| 2 | 53 | 0.70 | 0.98 | 19 | empty |
| 3 | 51 | 0.69 | 0.97 | 19 | GOL |
| 4 | 288 | 0.62 | 0.80 | 32 | I9G |
| 5 | 153 | 0.61 | 0.84 | 36 | empty |
Interfaces
4 interfaces between chains.
- A–B · 300 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 203 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 182 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 111 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 7KGY · Beta-glucuronidase from Faecalibacterium prausnitzii bound to the inhibitor… · 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
- Elsewhere: RCSB PDB 7KGY · PDBe 7KGY
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