MolNFT v1 · #18043 · protein
Crystal structure of a novel form of mistletoe lectin from himalayan viscum album L. at 3.8A resolution
1PC8 · Himalayan mistletoe ribosome-inactivating protein: “Crystal structure of a novel form of mistletoe lectin from himalayan viscum album L. at 3.8A resolution”. X-ray diffraction, 2 ligands (NAG, BMA), 5 pockets (best druggability…
- PDB
- 1PC8
- Type
- protein
- Length
- 495 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Himalayan mistletoe ribosome-inactivating protein
- EC
- 3.2.2.22
- Ligands
- NAG, BMA
- Pockets
- 5 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 23% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Himalayan mistletoe ribosome-inactivating protein (EC 3.2.2.22) | protein | 240 | 38% helix, 22% strand | — |
| B | Himalayan mistletoe ribosome-inactivating protein (EC 3.2.2.22) | protein | 255 | 10% helix, 40% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 7 copies · chains A, 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 252 | 0.70 | 0.86 | 49 | empty |
| 2 | 123 | 0.57 | 0.84 | 21 | empty |
| 3 | 142 | 0.56 | 0.82 | 29 | empty |
| 4 | 240 | 0.55 | 0.78 | 34 | empty |
| 5 | 160 | 0.51 | 0.78 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 1364 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 1PC8 · Crystal Structure of a novel form of mistletoe lectin from Himalayan Viscum album L. at… · 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 1PC8 · PDBe 1PC8
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