MolNFT v1 · #115118 · protein
Crystal structure of the glycosynthase mutant D324N of escherichia COLI GH63 glycosidase in complex with glucose and lactose
5CA3 · Glucosidase ygjk: “Crystal structure of the glycosynthase mutant D324N of escherichia COLI GH63 glycosidase in complex with…”. X-ray diffraction, 5 ligands (GLC, GAL, BGC), 14 pockets (best druggability 0.86). MolNFT v1 #115118 on…
- PDB
- 5CA3
- Type
- protein
- Length
- 1,517 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glucosidase ygjk
- EC
- 3.2.1.-
- UniProt
- P42592
- Ligands
- GLC, GAL, BGC, MG, CA
- Pockets
- 14 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glucosidase ygjk (EC 3.2.1.-) | protein | 758 | 34% helix, 24% strand | P42592 |
| B | Glucosidase ygjk (EC 3.2.1.-) | protein | 759 | 34% helix, 24% strand | P42592 |
Ligands and binding sites
- GLC · alpha-D-glucopyranose · sugar · 3 copies · chains A, B
- GAL · beta-D-galactopyranose · sugar · 2 copies · chains A, B
- BGC · beta-D-glucopyranose · sugar · chains B
- MG · Magnesium ion · metal · 3 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 948 | 0.86 | 0.88 | 128 | GLC, GAL, MG, BGC |
| 2 | 357 | 0.65 | 0.80 | 40 | empty |
| 3 | 110 | 0.62 | 0.87 | 20 | empty |
| 4 | 252 | 0.58 | 0.79 | 38 | empty |
| 5 | 84 | 0.56 | 0.86 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 1303 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 5CA3 · Crystal structure of the glycosynthase mutant D324N of Escherichia coli GH63 glycosidase… · the same entry in another collection · chain A against A, TM-score 1.00
- P42592 · AlphaFold monomer V2.0 prediction for glucosidase ygjk (P42592) · 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 P42592
- Elsewhere: RCSB PDB 5CA3 · PDBe 5CA3 · UniProt P42592
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.