Research workbench
Crystal structure of ribotoxin restrictocin complexed with a 29-mer SARCIN/RICIN domain RNA analog
Analyse Crystal structure of ribotoxin restrictocin complexed with a 29-mer… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1JBT
- Type
- protein + RNA
- Length
- 356 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 29-mer SARCIN/RICIN domain RNA analog; Restrictocin
- EC
- 3.1.27.-
- UniProt
- P67876
- Ligands
- K
- Pockets
- 4 · best druggability 0.66
Structure
x-ray diffraction · 2 distinct chains · 7% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, D | 29-mer SARCIN/RICIN domain RNA analog | rna | 29 | — | — |
| A, B | Restrictocin (EC 3.1.27.-) | protein | 149 | 7% helix, 30% strand | P67876 |
Ligands and binding sites
- K · Potassium ion · metal · 6 copies · chains C, A, D, 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 305 | 0.66 | 0.82 | 47 | K |
| 2 | 328 | 0.66 | 0.81 | 48 | K |
| 3 | 259 | 0.48 | 0.74 | 21 | K |
| 4 | 221 | 0.46 | 0.74 | 20 | K |
Interfaces
3 interfaces between chains.
- D–B · 670 Ų buried · 7 hydrogen bonds · protein-nucleic
- C–A · 633 Ų buried · 11 hydrogen bonds · protein-nucleic
- C–D · 186 Ų buried · 3 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 1JBT · Crystal structure of ribotoxin restrictocin complexed with a 29-mer SARCIN/RICIN domain… · the same entry in another collection · chain C against C, TM-score 1.00
- P67876 · AlphaFold monomer V2.0 prediction for ribonuclease mitogillin (P67876) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 P67876
- Elsewhere: RCSB PDB 1JBT · PDBe 1JBT · UniProt P67876
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