MolNFT v1 · #96979 · protein
Crystal structure of the bacillus subtilis pyrophosphohydrolase bsrpph bound to a non-hydrolysable triphosphorylated dinucleotide RNA (pcp- pgpg) - first guanosine residue in guanosine binding pocket
4JZU · RNA pyrophosphohydrolase: “Crystal structure of the bacillus subtilis pyrophosphohydrolase bsrpph bound to a non-hydrolysable…”. X-ray diffraction, 1 ligand (GCP), 3 pockets (best druggability 0.66). MolNFT v1 #96979 on GenesisL1…
- PDB
- 4JZU
- Type
- protein
- Length
- 308 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA pyrophosphohydrolase
- EC
- 3.6.1.55
- UniProt
- O35013
- Ligands
- GCP
- Pockets
- 3 · best druggability 0.66
Structure
x-ray diffraction · 2 distinct chains · 20% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RNA pyrophosphohydrolase (EC 3.6.1.55) | protein | 157 | 20% helix, 43% strand | O35013 |
| B | RNA pyrophosphohydrolase (EC 3.6.1.55) | protein | 151 | 20% helix, 42% strand | O35013 |
Ligands and binding sites
- GCP · Phosphomethylphosphonic acid guanylate ester · ligand · chains A
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 458 | 0.66 | 0.78 | 54 | empty |
| 2 | 183 | 0.48 | 0.76 | 34 | GCP |
| 3 | 53 | 0.24 | 0.72 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 332 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 4JZU · Crystal structure of the Bacillus subtilis pyrophosphohydrolase BsRppH bound to a… · the same entry in another collection · chain B against B, TM-score 1.00
- O35013 · AlphaFold monomer V2.0 prediction for putative 8-oxo-dgtp diphosphatase ytkd (O35013) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 O35013
- Elsewhere: RCSB PDB 4JZU · PDBe 4JZU · UniProt O35013
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