MolNFT v1 · #32658 · protein + RNA
Catalytic domain of E. COLI RNase E
2BX2 · Ribonuclease E: “Catalytic domain of E. COLI RNase E”. X-ray diffraction, 2 ligands (MG, ZN), 7 pockets (best druggability 0.79). MolNFT v1 #32658 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2BX2
- Type
- protein + RNA
- Length
- 514 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribonuclease E; RNA (5'-R(*UP*UP*UP*AP*CP*AP*GP*UP*AP*UP*UP* UP*GP*UP*U)-3')
- EC
- 3.1.4.-
- UniProt
- P21513
- Ligands
- MG, ZN
- Pockets
- 7 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Ribonuclease E (EC 3.1.4.-) | protein | 500 | 32% helix, 26% strand | P21513 |
| R | RNA (5'-R(*UP*UP*UP*AP*CP*AP*GP*UP*AP*UP*UP* UP*GP*UP*U)-3') | rna | 14 | — | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 969 | 0.79 | 0.81 | 102 | empty |
| 2 | 76 | 0.60 | 0.89 | 21 | empty |
| 3 | 212 | 0.52 | 0.77 | 28 | empty |
| 4 | 85 | 0.45 | 0.80 | 16 | empty |
| 5 | 154 | 0.44 | 0.76 | 22 | empty |
Interfaces
1 interface between chains.
- L–R · 458 Ų buried · 12 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 2BX2 · PDBe 2BX2 · UniProt P21513
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