MolNFT v1 · #50263 · protein
Structural basis for the regulation of N-acetylglutamate kinase by pii in arabidopsis thaliana
2RD5 · Acetylglutamate kinase-like protein: “Structural basis for the regulation of N-acetylglutamate kinase by pii in arabidopsis thaliana”. X-ray diffraction, 5 ligands (ARG, ADP, NLG), 14 pockets (best druggability 0.66). MolNFT v1…
- PDB
- 2RD5
- Type
- protein
- Length
- 815 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acetylglutamate kinase-like protein; Pii protein
- EC
- 2.7.2.8
- UniProt
- Q9SCL7, Q9ZST4
- Ligands
- ARG, ADP, NLG, ATP, MG
- Pockets
- 14 · best druggability 0.66
Structure
x-ray diffraction · 4 distinct chains · 39% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Acetylglutamate kinase-like protein (EC 2.7.2.8) | protein | 281 | 45% helix, 25% strand | Q9SCL7 |
| B | Acetylglutamate kinase-like protein (EC 2.7.2.8) | protein | 283 | 44% helix, 23% strand | Q9SCL7 |
| C | Pii protein | protein | 125 | 26% helix, 34% strand | Q9ZST4 |
| D | Pii protein | protein | 126 | 26% helix, 33% strand | Q9ZST4 |
Ligands and binding sites
- ARG · Arginine · ligand · 2 copies · chains A, B
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
- NLG · N-acetyl-L-glutamate · ligand · 2 copies · chains A, B
- ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains C, D
- MG · Magnesium ion · metal · 3 copies · chains B, 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 | 463 | 0.66 | 0.78 | 50 | ADP, NLG |
| 2 | 287 | 0.65 | 0.81 | 40 | MG, ADP, NLG |
| 3 | 297 | 0.58 | 0.77 | 43 | empty |
| 4 | 232 | 0.54 | 0.77 | 33 | empty |
| 5 | 106 | 0.48 | 0.80 | 15 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1328 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 635 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 580 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 2RD5 · Structural basis for the regulation of N-acetylglutamate kinase by PII in Arabidopsis… · the same entry in another collection · chain D against D, TM-score 1.00
- Q9SCL7 · AlphaFold monomer V2.0 prediction for acetylglutamate kinase, chloroplastic (Q9SCL7) · a predicted model of the same protein · chain A against A, TM-score 0.99
- Q9ZST4 · AlphaFold monomer V2.0 prediction for nitrogen regulatory protein P-II homolog (Q9ZST4) · a predicted model of the same protein · chain D against A, TM-score 0.97
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 Q9ZST4
- Elsewhere: RCSB PDB 2RD5 · PDBe 2RD5 · UniProt Q9SCL7 · UniProt Q9ZST4
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