MolNFT v1 · #4051 · protein
Maackia amurensis leukoagglutinin (lectin) with sialyllactose
1DBN · Protein (leukoagglutinin): “Maackia amurensis leukoagglutinin (lectin) with sialyllactose”. X-ray diffraction, 6 ligands (NAG, BGC, GAL), 3 pockets (best druggability 0.63). MolNFT v1 #4051 on GenesisL1: 3D structure, binding sites…
- PDB
- 1DBN
- Type
- protein
- Length
- 478 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein (leukoagglutinin)
- Ligands
- NAG, BGC, GAL, SIA, CA, MN
- Pockets
- 3 · best druggability 0.63
Structure
x-ray diffraction · 1 distinct chain · 5% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Protein (leukoagglutinin) | protein | 239 | 5% helix, 44% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A, B
- BGC · beta-D-glucopyranose · sugar · 2 copies · chains A, B
- GAL · beta-D-galactopyranose · sugar · 2 copies · chains A, B
- SIA · N-acetyl-alpha-neuraminic acid · sugar · 2 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, B
- MN · Manganese (II) ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 569 | 0.63 | 0.75 | 66 | empty |
| 2 | 68 | 0.34 | 0.76 | 13 | GAL |
| 3 | 57 | 0.33 | 0.77 | 14 | GAL |
Interfaces
1 interface between chains.
- A–B · 715 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 glycan (N-glycosylation).
Compared structures
- 1DBN · Maackia amurensis leukoagglutinin (lectin) with sialyllactose · 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
- Elsewhere: RCSB PDB 1DBN · PDBe 1DBN
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.