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The structure of the pii protein from the cyanobacteria synechococcus sp. pcc 7942
Analyse The structure of the pii protein from the cyanobacteria synechococcus sp. pcc… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1QY7
- Type
- protein
- Length
- 336 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nitrogen regulatory protein P-II
- UniProt
- P0A3F4
- Ligands
- NI, SO4
- Pockets
- 5 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 25% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Nitrogen regulatory protein P-II | protein | 112 | 25% helix, 42% strand | P0A3F4 |
Ligands and binding sites
- NI · Nickel (II) ion · metal · 3 copies · chains A, B, C
- SO4 · Sulfate ion · ion · 6 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 57 | 0.71 | 0.98 | 30 | empty |
| 2 | 387 | 0.63 | 0.78 | 42 | SO4 |
| 3 | 341 | 0.62 | 0.78 | 42 | SO4 |
| 4 | 326 | 0.62 | 0.79 | 43 | SO4 |
| 5 | 131 | 0.48 | 0.79 | 30 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1131 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 1130 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 1129 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 1QY7 · The structure of the PII protein from the cyanobacteria Synechococcus sp. PCC 7942 · the same entry in another collection · chain A against A, TM-score 1.00
- P0A3F4 · AlphaFold monomer V2.0 prediction for nitrogen regulatory protein P-II (P0A3F4) · a predicted model of the same protein · chain A against A, TM-score 0.81
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 P0A3F4
- Elsewhere: RCSB PDB 1QY7 · PDBe 1QY7 · UniProt P0A3F4
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