Research workbench
Structure of E. COLI rpph bound to RNA and two magnesium ions
Analyse Structure of E. COLI rpph bound to RNA and two magnesium ions in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4S2X
- Type
- protein + RNA
- Length
- 160 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA pyrophosphohydrolase; RNA (5'-R(*(APC)*GP*U)-3')
- EC
- 3.6.1.-
- UniProt
- P0A776
- Ligands
- MG, SO4
- Pockets
- 1 · best druggability 0.34
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RNA pyrophosphohydrolase (EC 3.6.1.-) | protein | 158 | 31% helix, 32% strand | P0A776 |
| B | RNA (5'-R(*(APC)*GP*U)-3') | rna | 2 | — | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 56 | 0.34 | 0.78 | 11 | empty |
Interfaces
1 interface between chains.
- A–B · 463 Ų buried · 20 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
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 P0A776
- Elsewhere: RCSB PDB 4S2X · PDBe 4S2X · UniProt P0A776
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