Research workbench
Crystal structure of plant lectin (ligand-bound form)
Analyse Crystal structure of plant lectin (ligand-bound form) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3WCS
- Type
- protein
- Length
- 478 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Erythroagglutinin
- UniProt
- V5YN37
- Ligands
- NAG, MAN, GAL, MN, CA
- Pockets
- 1 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 5% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Erythroagglutinin | protein | 238 | 4% helix, 46% strand | V5YN37 |
| B | Erythroagglutinin | protein | 240 | 6% helix, 45% strand | V5YN37 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · 2 copies · chains A, B
- GAL · beta-D-galactopyranose · sugar · chains A
- MN · Manganese (II) ion · metal · 2 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 5 copies · chains A, 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 506 | 0.75 | 0.84 | 66 | EDO |
Interfaces
1 interface between chains.
- A–B · 994 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 glycan (N-glycosylation).
Compared structures
- 3WCS · Crystal structure of plant lectin (ligand-bound form) · 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 V5YN37
- Elsewhere: RCSB PDB 3WCS · PDBe 3WCS · UniProt V5YN37
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