Research workbench
Crystal structure of the ribotoxin restrictocin and a 31- mer srd RNA inhibitor
Analyse Crystal structure of the ribotoxin restrictocin and a 31- mer srd RNA inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1JBR
- Type
- protein + RNA
- Length
- 360 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'- R(*GP*CP*GP*CP*UP*CP*CP*UP*CP*AP*GP*UP*AP*CP*GP*AP*GP*(A23) )-3'…
- EC
- 3.1.27.-
- UniProt
- P67876
- Ligands
- K
- Pockets
- 7 · best druggability 0.50
Structure
x-ray diffraction · 4 distinct chains · 9% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | 5'- R(*GP*CP*GP*CP*UP*CP*CP*UP*CP*AP*GP*UP*AP*CP*GP*AP*GP*(A23) )-3' | rna | 18 | — | — |
| F | 5'-R(*GP*GP*AP*AP*CP*CP*GP*GP*AP*GP*CP*GP*C)-3' | rna | 13 | — | — |
| D | 31-mer srd RNA analog | rna | 31 | — | — |
| A, B | Restrictocin (EC 3.1.27.-) | protein | 149 | 9% helix, 36% strand | P67876 |
Ligands and binding sites
- K · Potassium ion · metal · 5 copies · chains C, F, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 150 | 0.50 | 0.79 | 21 | K |
| 2 | 136 | 0.50 | 0.80 | 26 | empty |
| 3 | 142 | 0.39 | 0.74 | 17 | K |
| 4 | 65 | 0.33 | 0.76 | 13 | empty |
| 5 | 51 | 0.31 | 0.77 | 13 | empty |
Interfaces
6 interfaces between chains.
- C–F · 882 Ų buried · 71 hydrogen bonds · nucleic-nucleic
- D–B · 763 Ų buried · 10 hydrogen bonds · protein-nucleic
- C–A · 671 Ų buried · 19 hydrogen bonds · protein-nucleic
- C–D · 137 Ų buried · 6 hydrogen bonds · nucleic-nucleic
- F–D · 82 Ų buried · 2 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 4 disulfide, 1 modified (disulfide, nucleotide modification).
Compared structures
- 1JBR · Crystal Structure of the Ribotoxin Restrictocin and a 31-mer SRD RNA Inhibitor · 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 0.99
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 1JBR · PDBe 1JBR · UniProt P67876
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