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Crystal structure of the glycosynthase mutant D324N of escherichia COLI GH63 glycosidase in complex with glucose and lactose
Analyse Crystal structure of the glycosynthase mutant D324N of escherichia COLI GH63… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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
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