MolNFT v1 · #54619 · protein
Structure of pii from synechococcus elongatus in complex with 2-oxoglutarate at high 2-og concentrations
2XUL · Nitrogen regulatory protein P-II: “Structure of pii from synechococcus elongatus in complex with 2-oxoglutarate at high 2-og concentrations”. X-ray diffraction, 3 ligands (ATP, AKG, MG), 8 pockets (best druggability 0.80). MolNFT v1…
- PDB
- 2XUL
- Type
- protein
- Length
- 645 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nitrogen regulatory protein P-II
- UniProt
- P0A3F4
- Ligands
- ATP, AKG, MG
- Pockets
- 8 · best druggability 0.80
Structure
x-ray diffraction · 5 distinct chains · 30% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nitrogen regulatory protein P-II | protein | 106 | 30% helix, 35% strand | P0A3F4 |
| B | Nitrogen regulatory protein P-II | protein | 111 | 29% helix, 33% strand | P0A3F4 |
| C, F | Nitrogen regulatory protein P-II | protein | 107 | 31% helix, 36% strand | P0A3F4 |
| D | Nitrogen regulatory protein P-II | protein | 106 | 30% helix, 35% strand | P0A3F4 |
| E | Nitrogen regulatory protein P-II | protein | 108 | 29% helix, 35% strand | P0A3F4 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 6 copies · chains A, B, C, D, E, F
- AKG · 2-oxoglutaric acid · ligand · 6 copies · chains A, B, C, D, E, F
- MG · Magnesium ion · metal · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 244 | 0.80 | 0.92 | 44 | ATP, AKG, MG |
| 2 | 205 | 0.78 | 0.93 | 41 | ATP, AKG, MG |
| 3 | 212 | 0.78 | 0.92 | 41 | ATP, AKG, MG |
| 4 | 239 | 0.77 | 0.91 | 42 | ATP, AKG, MG |
| 5 | 228 | 0.77 | 0.91 | 40 | ATP, AKG, MG |
Interfaces
6 interfaces between chains.
- D–F · 1378 Ų buried · 23 hydrogen bonds · protein-protein
- A–C · 1364 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 1354 Ų buried · 23 hydrogen bonds · protein-protein
- E–F · 1342 Ų buried · 24 hydrogen bonds · protein-protein
- D–E · 1330 Ų buried · 24 hydrogen bonds · protein-protein
Compared structures
- 2XUL · Structure of PII from Synechococcus elongatus in complex with 2- oxoglutarate at high… · the same entry in another collection · chain F against F, 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 0.92
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 2XUL · PDBe 2XUL · UniProt P0A3F4
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