MolNFT v1 · #106561 · protein + RNA
Structure of E. COLI rpph bound to RNA and two magnesium ions
4S2X · RNA pyrophosphohydrolase: “Structure of E. COLI rpph bound to RNA and two magnesium ions”. X-ray diffraction, 2 ligands (MG, SO4), 1 pocket (best druggability 0.34). MolNFT v1 #106561 on GenesisL1: 3D structure, binding sites and…
- 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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