MolNFT v1 · #96980 · protein + RNA
Crystal structure of the bacillus subtilis pyrophosphohydrolase bsrpph bound to a non-hydrolysable triphosphorylated dinucleotide RNA (pcp- pgpg) - second guanosine residue in guanosine binding pocket
4JZV · RNA pyrophosphohydrolase: “Crystal structure of the bacillus subtilis pyrophosphohydrolase bsrpph bound to a non-hydrolysable…”. X-ray diffraction, 2 ligands (GCP, MG), 2 pockets (best druggability 0.67). MolNFT v1 #96980 on…
- PDB
- 4JZV
- Type
- protein + RNA
- Length
- 311 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA pyrophosphohydrolase; RNA (5'-R(*(GCP)P*G)-3')
- EC
- 3.6.1.55
- UniProt
- O35013
- Ligands
- GCP, MG
- Pockets
- 2 · best druggability 0.67
Structure
x-ray diffraction · 3 distinct chains · 19% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RNA pyrophosphohydrolase (EC 3.6.1.55) | protein | 158 | 20% helix, 42% strand | O35013 |
| B | RNA pyrophosphohydrolase (EC 3.6.1.55) | protein | 152 | 18% helix, 43% strand | O35013 |
| C | RNA (5'-R(*(GCP)P*G)-3') | rna | 1 | — | — |
Ligands and binding sites
- GCP · Phosphomethylphosphonic acid guanylate ester · ligand · chains A, C
- MG · Magnesium ion · metal · 3 copies · chains A, B
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 667 | 0.67 | 0.76 | 57 | empty |
| 2 | 85 | 0.40 | 0.78 | 18 | GCP, MG |
Interfaces
2 interfaces between chains.
- A–B · 316 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 287 Ų buried · 5 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 4JZV · Crystal structure of the Bacillus subtilis pyrophosphohydrolase BsRppH bound to a… · the same entry in another collection · chain A against A, 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 4JZV · PDBe 4JZV · UniProt O35013
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