Research workbench
Crystal structure of ricin bound with dinucleotide apg
Analyse Crystal structure of ricin bound with dinucleotide apg in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3RTJ
- Type
- protein + RNA
- Length
- 522 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA (5'-R(*AP*G)-3'); Ricin a chain; Ricin B chain
- EC
- 3.2.2.22
- UniProt
- P02879
- Ligands
- NAG, BGC, GAL
- Pockets
- 4 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 23% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D | RNA (5'-R(*AP*G)-3') | rna | 2 | — | — |
| A | Ricin a chain (EC 3.2.2.22) | protein | 258 | 36% helix, 24% strand | P02879 |
| B | Ricin B chain (EC 3.2.2.22) | protein | 262 | 9% helix, 37% strand | P02879 |
Ligands and binding sites
- 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 | 258 | 0.83 | 0.94 | 43 | empty |
| 2 | 471 | 0.67 | 0.79 | 56 | empty |
| 3 | 238 | 0.61 | 0.81 | 33 | empty |
| 4 | 116 | 0.35 | 0.73 | 21 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1649 Ų buried · 21 hydrogen bonds · protein-protein
- D–A · 390 Ų buried · 14 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 5 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 3RTJ · Crystal structure of ricin bound with dinucleotide ApG · 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 3RTJ · PDBe 3RTJ · UniProt P02879
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