Research workbench
Crystal structure of sambucus nigra agglutinin II (sna-II)-tetragonal crystal form- complexed to N-acetylgalactosamine
Analyse Crystal structure of sambucus nigra agglutinin II (sna-II)-tetragonal crystal… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3CA3
- Type
- protein
- Length
- 257 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Agglutinin II
- UniProt
- P33183
- Ligands
- NAG, FUC, A2G, NGA, SO4
- Pockets
- 1 · best druggability 0.47
Structure
x-ray diffraction · 1 distinct chain · 13% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Agglutinin II | protein | 257 | 13% helix, 37% strand | P33183 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 7 copies · chains A
- FUC · alpha-L-fucopyranose · sugar · 2 copies
- A2G · 2-acetamido-2-deoxy-alpha-D-galactopyranose · sugar · 2 copies · chains A
- NGA · 2-acetamido-2-deoxy-beta-D-galactopyranose · sugar · 2 copies · chains A
- SO4 · Sulfate ion · ion · 7 copies · chains A
- ACT · Acetate ion · additive · chains A
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 | 116 | 0.47 | 0.79 | 18 | empty |
Modifications
Observed in the structure: 4 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 3CA3 · Crystal structure of Sambucus Nigra Agglutinin II (SNA-II)-tetragonal crystal form… · the same entry in another collection · chain A against A, TM-score 1.00
- P33183 · AlphaFold monomer V2.0 prediction for nigrin B (P33183) · a predicted model of the same protein · chain A 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 P33183
- Elsewhere: RCSB PDB 3CA3 · PDBe 3CA3 · UniProt P33183
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