MolNFT v2 · #108004 · protein
N-acetylglutamate kinase from Arabidopsis thaliana in complex with PII from Chlamydomonas reinhardtii
4USJ · Acetylglutamate kinase, chloroplastic: “N-acetylglutamate kinase from Arabidopsis thaliana in complex with PII from Chlamydomonas reinhardtii”. X-ray diffraction at 2.85, 7 ligands (ARG, ATP, GLN), 14 pockets (best druggability…
- PDB
- 4USJ
- Type
- protein
- Length
- 846 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.85
- Source
- ARABIDOPSIS THALIANA; CHLAMYDOMONAS REINHARDTII
- Molecule
- Acetylglutamate kinase, chloroplastic; Nitrogen regulatory protein pii
- EC
- 2.7.2.8
- UniProt
- Q9SCL7, A8JI83
- Ligands
- ARG, ATP, GLN, ADP, NLG, X2W, MG
- Pockets
- 14 · best druggability 0.65
Structure
x-ray diffraction · resolution 2.85 · 2 distinct chains · 39% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Acetylglutamate kinase, chloroplastic (EC 2.7.2.8) | protein | 281 | 43% helix, 23% strand | Q9SCL7 |
| C, D | Nitrogen regulatory protein pii | protein | 142 | 29% helix, 30% strand | A8JI83 |
Ligands and binding sites
- ARG · Arginine · ligand · 2 copies · chains A, B
- ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains C, D
- GLN · Glutamine · ligand · 2 copies · chains C, D
- ADP · Adenosine-5'-diphosphate · ligand · chains A
- NLG · N-acetyl-L-glutamate · ligand · chains A
- X2W · N-acetyl-L-glutamyl 5-phosphate · ligand · chains B
- MG · Magnesium ion · metal · 3 copies · chains A, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 296 | 0.65 | 0.81 | 40 | ADP, NLG, MG |
| 2 | 441 | 0.65 | 0.78 | 57 | X2W |
| 3 | 290 | 0.57 | 0.77 | 43 | empty |
| 4 | 255 | 0.56 | 0.77 | 34 | empty |
| 5 | 99 | 0.49 | 0.82 | 24 | GLN |
Interfaces
3 interfaces between chains.
- A–B · 1349 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 644 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 525 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 4USJ · N-acetylglutamate kinase from arabidopsis thaliana in complex with pii from chlamydomonas… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9SCL7 · AlphaFold monomer V2.0 prediction for acetylglutamate kinase, chloroplastic (Q9SCL7) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 Q9SCL7
- Every structure of UniProt A8JI83
- Elsewhere: RCSB PDB 4USJ · PDBe 4USJ · UniProt Q9SCL7 · UniProt A8JI83
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