MolNFT v1 · #28471 · protein
Crystal structure of himalayan mistletoe rip reveals the presence of a natural inhibitor and a new functionally active sugar-binding site
1YF8 · Beta-galactoside-specific lectin 4: “Crystal structure of himalayan mistletoe rip reveals the presence of a natural inhibitor and a new…”. X-ray diffraction, 6 ligands (P6C, NAG, GAL), 5 pockets (best druggability 0.75). MolNFT v1…
- PDB
- 1YF8
- Type
- protein
- Length
- 495 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-galactoside-specific lectin 4
- EC
- 3.2.2.22
- UniProt
- Q6ITZ3
- Ligands
- P6C, NAG, GAL, MAN, BGC, BMA
- Pockets
- 5 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 24% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-galactoside-specific lectin 4 (EC 3.2.2.22) | protein | 240 | 39% helix, 24% strand | Q6ITZ3 |
| B | Beta-galactoside-specific lectin 4 (EC 3.2.2.22) | protein | 255 | 11% helix, 39% strand | Q6ITZ3 |
Ligands and binding sites
- P6C · 2-amino-4-isopropyl-pteridine-6-carboxylic acid · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 7 copies · chains B, A
- GAL · beta-D-galactopyranose · sugar · 3 copies · chains B
- MAN · alpha-D-mannopyranose · sugar · 2 copies
- BGC · beta-D-glucopyranose · sugar · 2 copies · chains B
- BMA · beta-D-mannopyranose · sugar
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 269 | 0.75 | 0.88 | 41 | empty |
| 2 | 150 | 0.60 | 0.84 | 24 | P6C |
| 3 | 190 | 0.53 | 0.78 | 31 | empty |
| 4 | 168 | 0.51 | 0.78 | 25 | empty |
| 5 | 56 | 0.46 | 0.84 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 1348 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 1YF8 · Crystal structure of Himalayan mistletoe RIP reveals the presence of a natural inhibitor… · the same entry in another collection · chain A against A, TM-score 1.00
- Q6ITZ3 · AlphaFold monomer V2.0 prediction for beta-galactoside-specific lectin 4 (Q6ITZ3) · a predicted model of the same protein · chain B 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 Q6ITZ3
- Elsewhere: RCSB PDB 1YF8 · PDBe 1YF8 · UniProt Q6ITZ3
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