Research workbench
Crystal structure of ricin bound with formycin monophosphate
Analyse Crystal structure of ricin bound with formycin monophosphate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3RTI
- Type
- protein
- Length
- 516 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ricin
- EC
- 3.2.2.22
- UniProt
- P02879
- Ligands
- FMP, NAG, BGC, GAL
- Pockets
- 4 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 25% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ricin (EC 3.2.2.22) | protein | 257 | 38% helix, 24% strand | P02879 |
| B | Ricin (EC 3.2.2.22) | protein | 259 | 12% helix, 36% strand | P02879 |
Ligands and binding sites
- FMP · Formycin-5'-monophosphate · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains B, A
- BGC · beta-D-glucopyranose · sugar · 2 copies · chains B
- GAL · beta-D-galactopyranose · sugar · 2 copies · chains B
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 | 266 | 0.80 | 0.92 | 44 | empty |
| 2 | 443 | 0.67 | 0.79 | 52 | empty |
| 3 | 243 | 0.57 | 0.78 | 39 | FMP |
| 4 | 97 | 0.35 | 0.74 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1638 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 3RTI · Crystal structure of ricin bound with formycin monophosphate · 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 P02879
- Elsewhere: RCSB PDB 3RTI · PDBe 3RTI · UniProt P02879
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