MolNFT v1 · #68714 · protein
Crystal structure of E. COLI beta-glucuronidase with the glucaro-D- lactam inhibitor bound
3K4D: “Crystal structure of E. COLI beta-glucuronidase with the glucaro-D- lactam inhibitor bound”. X-ray diffraction, 1 ligand (EVA), 15 pockets (best druggability 0.87). MolNFT v1 #68714 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3K4D
- Type
- protein
- Length
- 1,192 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-glucuronidase
- EC
- 3.2.1.31
- UniProt
- P05804
- Ligands
- EVA
- Pockets
- 15 · best druggability 0.87
Structure
x-ray diffraction · 1 distinct chain · 20% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Beta-glucuronidase (EC 3.2.1.31) | protein | 596 | 20% helix, 31% strand | P05804 |
Ligands and binding sites
- EVA · (2S,3R,4S,5R)-3,4,5-trihydroxy-6-oxopiperidine-2-carboxylic acid · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 933 | 0.87 | 0.88 | 101 | empty |
| 2 | 84 | 0.73 | 0.96 | 19 | empty |
| 3 | 286 | 0.66 | 0.82 | 35 | EVA |
| 4 | 635 | 0.66 | 0.76 | 71 | empty |
| 5 | 282 | 0.65 | 0.82 | 37 | EVA |
Interfaces
1 interface between chains.
- A–B · 1838 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 3K4D · Crystal structure of E. coli beta-glucuronidase with the glucaro-d-lactam inhibitor bound · the same entry in another collection · chain A against A, TM-score 1.00
- P05804 · AlphaFold monomer V2.0 prediction for beta-glucuronidase (P05804) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 P05804
- Elsewhere: RCSB PDB 3K4D · PDBe 3K4D · UniProt P05804
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