Research workbench
The structure of E. COLI RNase E catalytically inactive mutant with RNA bound
Analyse The structure of E. COLI RNase E catalytically inactive mutant with RNA bound in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5F6C
- Type
- protein + RNA
- Length
- 1,027 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribonuclease E; RNA (5'-R(P*GP*U)-3'); RNA (5'-R(P*GP*UP*G)-3')
- EC
- 3.1.26.12
- UniProt
- P21513
- Ligands
- MG, ZN
- Pockets
- 15 · best druggability 0.68
Structure
x-ray diffraction · 4 distinct chains · 31% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribonuclease E (EC 3.1.26.12) | protein | 512 | 31% helix, 24% strand | P21513 |
| B | Ribonuclease E (EC 3.1.26.12) | protein | 510 | 31% helix, 26% strand | P21513 |
| C | RNA (5'-R(P*GP*U)-3') | rna | 2 | — | — |
| E | RNA (5'-R(P*GP*UP*G)-3') | rna | 3 | — | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 468 | 0.68 | 0.80 | 51 | empty |
| 2 | 442 | 0.65 | 0.78 | 47 | empty |
| 3 | 355 | 0.61 | 0.78 | 42 | empty |
| 4 | 157 | 0.60 | 0.83 | 28 | empty |
| 5 | 279 | 0.57 | 0.78 | 35 | empty |
Interfaces
3 interfaces between chains.
- A–B · 3016 Ų buried · 48 hydrogen bonds · protein-protein
- A–E · 463 Ų buried · 6 hydrogen bonds · protein-nucleic
- B–C · 369 Ų buried · 13 hydrogen bonds · protein-nucleic
Compared structures
- 5F6C · The structure of E. coli RNase E catalytically inactive mutant with RNA bound · the same entry in another collection · chain E against E, TM-score 1.00
- 5F6C · The structure of E. coli RNase E catalytically inactive mutant with RNA bound · the same entry in another collection · chain A against A, TM-score 1.00
- P21513 · AlphaFold monomer V2.0 prediction for ribonuclease E (P21513) · a predicted model of the same protein · chain A against A, TM-score 0.78
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 P21513
- Elsewhere: RCSB PDB 5F6C · PDBe 5F6C · UniProt P21513
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.