MolNFT v1 · #30815 · protein
Crystallographic refinement of ricin to 2.5 ångströms
2AAI · Ricin (a chain): “Crystallographic refinement of ricin to 2.5 ångströms”. X-ray diffraction, 5 ligands (NAG, MAN, BGC), 4 pockets (best druggability 0.82). MolNFT v1 #30815 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 2AAI
- Type
- protein
- Length
- 529 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ricin (a chain); Ricin (B chain)
- EC
- 3.2.2.22
- UniProt
- P02879
- Ligands
- NAG, MAN, BGC, GAL, BMA
- Pockets
- 4 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 23% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ricin (a chain) (EC 3.2.2.22) | protein | 267 | 36% helix, 18% strand | P02879 |
| B | Ricin (B chain) (EC 3.2.2.22) | protein | 262 | 10% helix, 37% strand | P02879 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains B, A
- MAN · alpha-D-mannopyranose · sugar · 4 copies · chains A
- BGC · beta-D-glucopyranose · sugar · 2 copies · chains B
- GAL · beta-D-galactopyranose · sugar · 2 copies · chains B
- BMA · beta-D-mannopyranose · sugar · 2 copies
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 320 | 0.82 | 0.92 | 50 | empty |
| 2 | 512 | 0.70 | 0.80 | 59 | empty |
| 3 | 303 | 0.58 | 0.77 | 33 | empty |
| 4 | 97 | 0.39 | 0.76 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1645 Ų buried · 23 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 2AAI · Crystallographic refinement of ricin to 2.5 Angstroms · the same entry in another collection · chain B against B, 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 P02879
- Elsewhere: RCSB PDB 2AAI · PDBe 2AAI · UniProt P02879
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.