MolNFT v1 · #12511 · protein
Mannose-specific agglutinin (lectin) from garlic (allium sativum) bulbs complexed with alpha-D-mannose
1KJ1 · Lectin I: “Mannose-specific agglutinin (lectin) from garlic (allium sativum) bulbs complexed with alpha-D-mannose”. X-ray diffraction, 1 ligand (MAN), 2 pockets (best druggability 0.52). MolNFT v1 #12511 on GenesisL1: 3D structure…
- PDB
- 1KJ1
- Type
- protein
- Length
- 436 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lectin I; Lectin II
- UniProt
- Q38789, Q38783
- Ligands
- MAN
- Pockets
- 2 · best druggability 0.52
Structure
x-ray diffraction · 2 distinct chains · 0% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, P | Lectin I | protein | 109 | 0% helix, 45% strand | Q38789 |
| D, Q | Lectin II | protein | 109 | 0% helix, 47% strand | Q38783 |
Ligands and binding sites
- MAN · alpha-D-mannopyranose · sugar · 14 copies · chains A, D, P, Q
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 309 | 0.52 | 0.74 | 44 | MAN |
| 2 | 84 | 0.31 | 0.73 | 18 | MAN |
Interfaces
4 interfaces between chains.
- A–D · 1648 Ų buried · 28 hydrogen bonds · protein-protein
- P–Q · 1642 Ų buried · 31 hydrogen bonds · protein-protein
- D–P · 158 Ų buried · 0 hydrogen bonds · protein-protein
- D–Q · 39 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 1KJ1 · Mannose-specific agglutinin (lectin) from garlic (allium sativum) bulbs complexed 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 Q38789
- Every structure of UniProt Q38783
- Elsewhere: RCSB PDB 1KJ1 · PDBe 1KJ1 · UniProt Q38789 · UniProt Q38783
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