Research workbench
Crystal structure of the E496A mutant of hsbgla in complex with 4- galactosyllactose
Analyse Crystal structure of the E496A mutant of hsbgla in complex with 4… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6M55
- Type
- protein
- Length
- 1,084 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-galactosidase-like enzyme
- UniProt
- Q564N5
- Ligands
- NAG, GAL, GLC, MAN
- Pockets
- 7 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Beta-galactosidase-like enzyme | protein | 542 | 45% helix, 12% strand | Q564N5 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, D
- GAL · beta-D-galactopyranose · sugar · 4 copies · chains A, D
- GLC · alpha-D-glucopyranose · sugar · 2 copies · chains A, D
- MAN · alpha-D-mannopyranose · sugar · 2 copies · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 412 | 0.74 | 0.84 | 49 | empty |
| 2 | 65 | 0.72 | 0.98 | 28 | empty |
| 3 | 598 | 0.70 | 0.78 | 62 | GLC, GAL |
| 4 | 544 | 0.68 | 0.78 | 64 | GLC, GAL |
| 5 | 61 | 0.31 | 0.75 | 15 | empty |
Interfaces
1 interface between chains.
- A–D · 1686 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 glycan, 6 disulfide (disulfide, N-glycosylation, O-glycosylation).
Compared structures
- 6M55 · Crystal structure of the E496A mutant of HsBglA in complex with 4-galactosyllactose · 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 Q564N5
- Elsewhere: RCSB PDB 6M55 · PDBe 6M55 · UniProt Q564N5
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