Research workbench
Structure of pii from synechococcus elongatus in complex with 2-oxoglutarate at low 2-og concentrations
Analyse Structure of pii from synechococcus elongatus in complex with 2-oxoglutarate at… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2XZW
- Type
- protein
- Length
- 965 residues
- Chains
- 9
- 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
- 12 · best druggability 0.82
Structure
x-ray diffraction · 9 distinct chains · 29% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nitrogen regulatory protein P-II | protein | 109 | 29% helix, 34% strand | P0A3F4 |
| B | Nitrogen regulatory protein P-II | protein | 111 | 29% helix, 34% strand | P0A3F4 |
| C | Nitrogen regulatory protein P-II | protein | 113 | 31% helix, 34% strand | P0A3F4 |
| D | Nitrogen regulatory protein P-II | protein | 105 | 30% helix, 36% strand | P0A3F4 |
| E | Nitrogen regulatory protein P-II | protein | 97 | 32% helix, 38% strand | P0A3F4 |
| F | Nitrogen regulatory protein P-II | protein | 108 | 30% helix, 35% strand | P0A3F4 |
| G | Nitrogen regulatory protein P-II | protein | 110 | 29% helix, 35% strand | P0A3F4 |
| H | Nitrogen regulatory protein P-II | protein | 109 | 26% helix, 35% strand | P0A3F4 |
| I | Nitrogen regulatory protein P-II | protein | 103 | 27% helix, 38% strand | P0A3F4 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 9 copies · chains A, B, C, D, E, F, G, H, I
- AKG · 2-oxoglutaric acid · ligand · 6 copies · chains A, B, C, F, H, E, I
- MG · Magnesium ion · metal · 6 copies · chains A, B, C, F, H, I
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 235 | 0.82 | 0.94 | 44 | ATP, AKG, MG |
| 2 | 236 | 0.81 | 0.94 | 47 | ATP, AKG, MG |
| 3 | 242 | 0.80 | 0.93 | 44 | ATP, AKG, MG |
| 4 | 237 | 0.79 | 0.92 | 39 | ATP, AKG, MG |
| 5 | 211 | 0.78 | 0.93 | 40 | ATP, AKG, MG |
Interfaces
13 interfaces between chains.
- A–B · 1367 Ų buried · 27 hydrogen bonds · protein-protein
- A–C · 1353 Ų buried · 26 hydrogen bonds · protein-protein
- G–I · 1301 Ų buried · 27 hydrogen bonds · protein-protein
- D–F · 1295 Ų buried · 30 hydrogen bonds · protein-protein
- H–I · 1281 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 2XZW · Structure of pii from synechococcus elongatus in complex with 2- oxoglutarate at low 2-og… · the same entry in another collection · chain I against I, 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 E against A, TM-score 0.98
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 2XZW · PDBe 2XZW · UniProt P0A3F4
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