Research workbench
Unusual, dual endo- and exo-nuclease activity in the degradosome explained by crystal structure analysis of RNase J1
Analyse Unusual, dual endo- and exo-nuclease activity in the degradosome explained by… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ZQ4
- Type
- protein
- Length
- 2,174 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribonuclease J 1
- EC
- 3.1.-.-
- UniProt
- Q45493
- Ligands
- ZN, CA
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 34% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribonuclease J 1 (EC 3.1.-.-) | protein | 550 | 33% helix, 26% strand | Q45493 |
| C | Ribonuclease J 1 (EC 3.1.-.-) | protein | 542 | 34% helix, 26% strand | Q45493 |
| D | Ribonuclease J 1 (EC 3.1.-.-) | protein | 538 | 34% helix, 27% strand | Q45493 |
| E | Ribonuclease J 1 (EC 3.1.-.-) | protein | 544 | 33% helix, 26% strand | Q45493 |
Ligands and binding sites
- ZN · Zinc ion · metal · 8 copies · chains A, C, D, E
- CA · Calcium ion · metal · 4 copies · chains A, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 775 | 0.76 | 0.80 | 86 | empty |
| 2 | 652 | 0.73 | 0.80 | 71 | empty |
| 3 | 318 | 0.69 | 0.83 | 40 | empty |
| 4 | 238 | 0.64 | 0.83 | 36 | ZN |
| 5 | 384 | 0.60 | 0.76 | 48 | empty |
Interfaces
6 interfaces between chains.
- A–C · 2698 Ų buried · 24 hydrogen bonds · protein-protein
- D–E · 2673 Ų buried · 30 hydrogen bonds · protein-protein
- A–E · 1062 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 1047 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 70 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 3ZQ4 · Unusual, dual endo- and exo-nuclease activity in the degradosome explained by crystal… · the same entry in another collection · chain E against E, TM-score 1.00
- Q45493 · AlphaFold monomer V2.0 prediction for ribonuclease J1 (Q45493) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 Q45493
- Elsewhere: RCSB PDB 3ZQ4 · PDBe 3ZQ4 · UniProt Q45493
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