Research workbench
Controlling the storage of nitrogen as arginine: the complex of PII and acetylglutamate kinase from Synechococcus elongatus PCC 7942
Analyse Controlling the storage of nitrogen as arginine: the complex of PII and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2V5H
- Type
- protein
- Length
- 2,371 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.75
- Source
- SYNECHOCOCCUS ELONGATUS
- Molecule
- Acetylglutamate kinase; Nitrogen regulatory protein P-II
- EC
- 2.7.2.8
- UniProt
- Q6V1L5, P0A3F4
- Ligands
- NLG, NA, CL
- Pockets
- 20 · best druggability 0.71
Structure
x-ray diffraction · resolution 2.75 · 9 distinct chains · 37% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Acetylglutamate kinase (EC 2.7.2.8) | protein | 284 | 42% helix, 23% strand | Q6V1L5 |
| B | Acetylglutamate kinase (EC 2.7.2.8) | protein | 289 | 42% helix, 24% strand | Q6V1L5 |
| D, E | Acetylglutamate kinase (EC 2.7.2.8) | protein | 286 | 43% helix, 24% strand | Q6V1L5 |
| F | Acetylglutamate kinase (EC 2.7.2.8) | protein | 287 | 41% helix, 24% strand | Q6V1L5 |
| G | Nitrogen regulatory protein P-II | protein | 111 | 25% helix, 41% strand | P0A3F4 |
| H, K | Nitrogen regulatory protein P-II | protein | 108 | 26% helix, 41% strand | P0A3F4 |
| I | Nitrogen regulatory protein P-II | protein | 109 | 26% helix, 40% strand | P0A3F4 |
| J | Nitrogen regulatory protein P-II | protein | 110 | 25% helix, 41% strand | P0A3F4 |
| L | Nitrogen regulatory protein P-II | protein | 109 | 26% helix, 42% strand | P0A3F4 |
Ligands and binding sites
- NLG · N-acetyl-L-glutamate · ligand · 6 copies · chains A, B, C, D, E, F
- NA · Sodium ion · metal · 6 copies · chains A, B, C, D, E, F
- CL · Chloride ion · ion · 6 copies · chains G, I, H, J, K, L
- GOL · Glycerol · additive · chains D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 229 | 0.71 | 0.87 | 37 | CL |
| 2 | 210 | 0.70 | 0.87 | 36 | CL |
| 3 | 203 | 0.69 | 0.86 | 37 | CL |
| 4 | 222 | 0.68 | 0.86 | 37 | CL |
| 5 | 207 | 0.68 | 0.86 | 34 | CL |
Interfaces
18 interfaces between chains.
- D–E · 1611 Ų buried · 16 hydrogen bonds · protein-protein
- C–F · 1607 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1599 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 1427 Ų buried · 11 hydrogen bonds · protein-protein
- D–F · 1418 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 2V5H · Controlling the storage of nitrogen as arginine: the complex of pii and acetylglutamate… · the same entry in another collection · chain L against L, TM-score 1.00
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 Q6V1L5
- Every structure of UniProt P0A3F4
- Elsewhere: RCSB PDB 2V5H · PDBe 2V5H · UniProt Q6V1L5 · UniProt P0A3F4
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