Research workbench
X-ray crystal structure of erythrina crista-galli lectin in complex with N-acetyllactosamine
Analyse X-ray crystal structure of erythrina crista-galli lectin in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6AQ6
- Type
- protein
- Length
- 478 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lectin
- UniProt
- Q6YD91
- Ligands
- NAG, GAL, BMA, XYP, MAN, FUC, CA, MN, NA
- Pockets
- 1 · best druggability 0.30
Structure
x-ray diffraction · 1 distinct chain · 3% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Lectin | protein | 239 | 3% helix, 44% strand | Q6YD91 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, B
- GAL · beta-D-galactopyranose · sugar · 2 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar
- XYP · beta-D-xylopyranose · sugar
- MAN · alpha-D-mannopyranose · sugar
- FUC · alpha-L-fucopyranose · sugar · chains A
- CA · Calcium ion · metal · 2 copies · chains A, B
- MN · Manganese (II) ion · metal · 2 copies · chains A, B
- NA · Sodium ion · metal · chains A
- ACT · Acetate ion · additive · 2 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 50 | 0.30 | 0.76 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 848 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 glycan (N-glycosylation).
Compared structures
- 6AQ6 · X-ray crystal structure of Erythrina crista-galli lectin in complex with… · 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 Q6YD91
- Elsewhere: RCSB PDB 6AQ6 · PDBe 6AQ6 · UniProt Q6YD91
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