Research workbench
1.75 ångström resolution crystal structure of a putative ntp pyrophosphohydrolase (yfao) from salmonella typhimurium LT2
Analyse 1.75 ångström resolution crystal structure of a putative ntp… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3OGA
- Type
- protein
- Length
- 263 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nucleoside triphosphatase nudi
- EC
- 3.6.1.-
- UniProt
- Q8ZNF5
- Ligands
- PO4
- Pockets
- 3 · best druggability 0.59
Structure
x-ray diffraction · 2 distinct chains · 22% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nucleoside triphosphatase nudi (EC 3.6.1.-) | protein | 134 | 21% helix, 47% strand | Q8ZNF5 |
| B | Nucleoside triphosphatase nudi (EC 3.6.1.-) | protein | 129 | 22% helix, 42% strand | Q8ZNF5 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 5 copies · chains A, B
- BME · Beta-mercaptoethanol · additive · 3 copies · chains A, 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 264 | 0.59 | 0.78 | 29 | BME, PO4 |
| 2 | 137 | 0.51 | 0.80 | 21 | empty |
| 3 | 179 | 0.51 | 0.78 | 25 | BME |
Interfaces
1 interface between chains.
- A–B · 839 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 covalent (additive adduct).
Compared structures
- 3OGA · 1.75 Angstrom resolution crystal structure of a putative NTP pyrophosphohydrolase (yfaO)… · the same entry in another collection · chain A against A, TM-score 1.00
- Q8ZNF5 · AlphaFold monomer V2.0 prediction for nucleoside triphosphatase nudi (Q8ZNF5) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 Q8ZNF5
- Elsewhere: RCSB PDB 3OGA · PDBe 3OGA · UniProt Q8ZNF5
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