Research workbench
Catalysis and 5' end sensing by ribonuclease RNase J of the metallo-beta-lactamase family
Analyse Catalysis and 5' end sensing by ribonuclease RNase J of the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5A0V
- Type
- protein + RNA
- Length
- 914 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribonuclease J; 5'-R(*CP*GP*CP*CP*UP*CP)-3'
- UniProt
- O86842
- Ligands
- C5P, ZN
- Pockets
- 10 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 29% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribonuclease J | protein | 454 | 29% helix, 25% strand | O86842 |
| B | Ribonuclease J | protein | 451 | 30% helix, 25% strand | O86842 |
| E | 5'-R(*CP*GP*CP*CP*UP*CP)-3' | rna | 5 | — | — |
| F | 5'-R(*CP*GP*CP*CP*UP*CP)-3' | rna | 4 | — | — |
Ligands and binding sites
- C5P · Cytidine-5'-monophosphate · ligand · chains B, F
- ZN · Zinc ion · metal · 4 copies · chains A, E, B, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 935 | 0.81 | 0.83 | 105 | C5P |
| 2 | 166 | 0.56 | 0.81 | 22 | empty |
| 3 | 267 | 0.52 | 0.75 | 40 | empty |
| 4 | 177 | 0.44 | 0.74 | 33 | empty |
| 5 | 58 | 0.44 | 0.83 | 16 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1222 Ų buried · 13 hydrogen bonds · protein-protein
- A–E · 1005 Ų buried · 15 hydrogen bonds · protein-nucleic
- B–F · 810 Ų buried · 18 hydrogen bonds · protein-nucleic
Compared structures
- 5A0V · Catalysis and 5' end sensing by ribonuclease RNase J of the metallo- beta-lactamase family · 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 O86842
- Elsewhere: RCSB PDB 5A0V · PDBe 5A0V · UniProt O86842
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