MolNFT v1 · #125377 · protein
A glycoside hydrolase mutant with an unreacted activity based probe bound
5L77 · Beta-glucuronidase: “A glycoside hydrolase mutant with an unreacted activity based probe bound”. X-ray diffraction, 3 ligands (GUX, PO4, CL), 5 pockets (best druggability 0.67). MolNFT v1 #125377 on GenesisL1: 3D structure, binding…
- PDB
- 5L77
- Type
- protein
- Length
- 458 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-glucuronidase
- UniProt
- C1F2K5
- Ligands
- GUX, PO4, CL
- Pockets
- 5 · best druggability 0.67
Structure
x-ray diffraction · 1 distinct chain · 30% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-glucuronidase | protein | 458 | 30% helix, 29% strand | C1F2K5 |
Ligands and binding sites
- GUX · (1~{R},2~{S},3~{R},4~{S},5~{S},6~{R})-7-[8-[(azanylidene-{4}-azanylidene)amino]octyl]-3,4,5-tris(oxidanyl)-7-azabicyclo[4.1.0]heptane-2-carboxylic acid · ligand · chains A
- PO4 · Phosphate ion · ion · 5 copies · chains A
- CL · Chloride ion · ion · chains A
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 341 | 0.67 | 0.81 | 36 | GUX |
| 2 | 110 | 0.46 | 0.79 | 31 | empty |
| 3 | 74 | 0.37 | 0.78 | 20 | empty |
| 4 | 68 | 0.31 | 0.75 | 17 | empty |
| 5 | 57 | 0.26 | 0.73 | 19 | empty |
Compared structures
- 5L77 · A glycoside hydrolase mutant with an unreacted activity based probe bound · 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 C1F2K5
- Elsewhere: RCSB PDB 5L77 · PDBe 5L77 · UniProt C1F2K5
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