MolNFT v1 · #155660 · protein
Structure of E. COLI beta-glucuronidase complex with C6-propyl uronic isofagomine
6LEJ · Beta-D-glucuronidase: “Structure of E. COLI beta-glucuronidase complex with C6-propyl uronic isofagomine”. X-ray diffraction, 1 ligand (CKX), 19 pockets (best druggability 0.86). MolNFT v1 #155660 on GenesisL1: 3D structure, binding…
- PDB
- 6LEJ
- Type
- protein
- Length
- 1,187 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-D-glucuronidase
- EC
- 3.2.1.31
- UniProt
- W8SYR0
- Ligands
- CKX
- Pockets
- 19 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 20% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-D-glucuronidase (EC 3.2.1.31) | protein | 600 | 20% helix, 31% strand | W8SYR0 |
| B | Beta-D-glucuronidase (EC 3.2.1.31) | protein | 587 | 20% helix, 29% strand | W8SYR0 |
Ligands and binding sites
- CKX · (2~{S},3~{S},4~{R},5~{R})-4,5-bis(oxidanyl)-2-propyl-piperidine-3-carboxylic acid · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1050 | 0.86 | 0.87 | 110 | empty |
| 2 | 592 | 0.73 | 0.80 | 56 | CKX |
| 3 | 75 | 0.72 | 0.96 | 20 | empty |
| 4 | 483 | 0.72 | 0.81 | 43 | CKX |
| 5 | 123 | 0.72 | 0.93 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 1712 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 6LEJ · Structure of E. coli beta-glucuronidase complex with C6-propyl 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 W8SYR0
- Elsewhere: RCSB PDB 6LEJ · PDBe 6LEJ · UniProt W8SYR0
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