Research workbench
Crystal structure of the Escherichia coli nucleosidase PpnN (pppGpp-form)
Analyse Crystal structure of the Escherichia coli nucleosidase PpnN (pppGpp-form) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6GFM
- Type
- protein
- Length
- 440 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.77
- Source
- Escherichia coli K-12
- Molecule
- Pyrimidine/purine nucleotide 5'-monophosphate nucleosidase
- EC
- 3.2.2.-, 3.2.2.10, 3.2.2.4
- UniProt
- P0ADR8
- Ligands
- 0O2
- Pockets
- 5 · best druggability 0.61
Structure
x-ray diffraction · resolution 2.77 · 1 distinct chain · 49% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pyrimidine/purine nucleotide 5'-monophosphate nucleosidase (EC 3.2.2.-, 3.2.2.10, 3.2.2.4) | protein | 440 | 49% helix, 12% strand | P0ADR8 |
Ligands and binding sites
- 0O2 · guanosine 5'-(tetrahydrogen triphosphate) 3'-(trihydrogen diphosphate) · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 424 | 0.61 | 0.76 | 42 | empty |
| 2 | 179 | 0.57 | 0.80 | 19 | empty |
| 3 | 134 | 0.47 | 0.78 | 24 | empty |
| 4 | 97 | 0.39 | 0.76 | 18 | empty |
| 5 | 83 | 0.37 | 0.77 | 17 | empty |
Compared structures
- 6GFM · Crystal structure of the escherichia COLI nucleosidase ppnn (pppgpp- form) · the same entry in another collection · chain A against A, TM-score 1.00
- P0ADR8 · AlphaFold monomer V2.0 prediction for PYRIMIDINE/PURINE nucleotide 5'-monophosphate… · a predicted model of the same protein · chain A against A, TM-score 0.90
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 P0ADR8
- Elsewhere: RCSB PDB 6GFM · PDBe 6GFM · UniProt P0ADR8
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