MolNFT v1 · #32923 · protein + RNA
Catalytic domain of E. COLI RNase E
2C4R · Ribonuclease E: “Catalytic domain of E. COLI RNase E”. X-ray diffraction, 2 ligands (MG, ZN), 4 pockets (best druggability 0.85). MolNFT v1 #32923 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2C4R
- Type
- protein + RNA
- Length
- 501 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribonuclease E; Ssrna molecule: 5'-R(*AP*CP*AP*GP*UP*AP*UP*UP*UP*GP)-3'
- EC
- 3.1.4.-
- UniProt
- P21513
- Ligands
- MG, ZN
- Pockets
- 4 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 29% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Ribonuclease E (EC 3.1.4.-) | protein | 491 | 29% helix, 22% strand | P21513 |
| R | Ssrna molecule: 5'-R(*AP*CP*AP*GP*UP*AP*UP*UP*UP*GP)-3' | rna | 10 | — | — |
Ligands and binding sites
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 | 1089 | 0.85 | 0.86 | 111 | empty |
| 2 | 89 | 0.58 | 0.87 | 21 | empty |
| 3 | 122 | 0.50 | 0.80 | 34 | empty |
| 4 | 61 | 0.41 | 0.81 | 15 | empty |
Interfaces
1 interface between chains.
- L–R · 899 Ų buried · 19 hydrogen bonds · protein-nucleic
Compared structures
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 2C4R · PDBe 2C4R · UniProt P21513
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