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Crystal structure of the amino acid kinase domain from saccharomyces cerevisiae acetylglutamate kinase in complex with its feed-back inhibitor L-arginine
Analyse Crystal structure of the amino acid kinase domain from saccharomyces cerevisiae… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ZZH
- Type
- protein
- Length
- 1,157 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acetylglutamate kinase
- EC
- 2.7.2.8
- UniProt
- Q01217
- Ligands
- NLG, ARG, CL
- Pockets
- 17 · best druggability 0.70
Structure
x-ray diffraction · 3 distinct chains · 47% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Acetylglutamate kinase (EC 2.7.2.8) | protein | 291 | 45% helix, 23% strand | Q01217 |
| B, D | Acetylglutamate kinase (EC 2.7.2.8) | protein | 289 | 46% helix, 21% strand | Q01217 |
| C | Acetylglutamate kinase (EC 2.7.2.8) | protein | 288 | 48% helix, 23% strand | Q01217 |
Ligands and binding sites
- NLG · N-acetyl-L-glutamate · ligand · 4 copies · chains A, B, C, D
- ARG · Arginine · ligand · chains C
- CL · Chloride ion · ion · 5 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 45 copies · chains A, B, D, C
- MLI · Malonate ion · additive · 3 copies · chains A, B, D
- GOL · Glycerol · additive · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 494 | 0.70 | 0.80 | 52 | EDO, CL, MLI, NLG |
| 2 | 459 | 0.69 | 0.80 | 55 | EDO, MLI, NLG |
| 3 | 417 | 0.68 | 0.80 | 43 | EDO, CL, NLG |
| 4 | 498 | 0.66 | 0.78 | 58 | EDO, NLG |
| 5 | 180 | 0.63 | 0.84 | 33 | EDO |
Interfaces
4 interfaces between chains.
- A–B · 1112 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 1109 Ų buried · 16 hydrogen bonds · protein-protein
- A–D · 918 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 844 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 3ZZH · Crystal structure of the amino acid kinase domain from Saccharomyces cerevisiae… · the same entry in another collection · chain D against D, TM-score 1.00
- Q01217 · AlphaFold monomer V2.0 prediction for protein ARG5,6, mitochondrial (Q01217) · a predicted model of the same protein · chain C against A, TM-score 0.95
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 Q01217
- Elsewhere: RCSB PDB 3ZZH · PDBe 3ZZH · UniProt Q01217
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