Research workbench
Crystal structure of the amino acid kinase domain from saccharomyces cerevisiae acetylglutamate kinase complexed with its substrate N-acetylglutamate
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
- 3ZZF
- Type
- protein
- Length
- 1,161 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, HG, CL
- Pockets
- 17 · best druggability 0.70
Structure
x-ray diffraction · 3 distinct chains · 46% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Acetylglutamate kinase (EC 2.7.2.8) | protein | 291 | 45% helix, 22% strand | Q01217 |
| B | Acetylglutamate kinase (EC 2.7.2.8) | protein | 289 | 46% helix, 22% strand | Q01217 |
| D | Acetylglutamate kinase (EC 2.7.2.8) | protein | 290 | 46% helix, 21% strand | Q01217 |
Ligands and binding sites
- NLG · N-acetyl-L-glutamate · ligand · 4 copies · chains A, B, C, D
- HG · Mercury (II) ion · metal · 8 copies · chains A, B, C, D
- CL · Chloride ion · ion · 7 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 13 copies · chains A, B, C, D
- GOL · Glycerol · additive · 4 copies · chains A, B, 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, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 447 | 0.70 | 0.81 | 49 | EDO, GOL, NLG |
| 2 | 336 | 0.69 | 0.83 | 50 | HG, CL |
| 3 | 462 | 0.68 | 0.79 | 53 | GOL, NLG |
| 4 | 347 | 0.67 | 0.81 | 41 | EDO, GOL, NLG |
| 5 | 417 | 0.67 | 0.79 | 42 | EDO, GOL, NLG |
Interfaces
4 interfaces between chains.
- C–D · 1058 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1036 Ų buried · 17 hydrogen bonds · protein-protein
- B–C · 966 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 965 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 3ZZF · 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 A against A, TM-score 0.91
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 3ZZF · PDBe 3ZZF · UniProt Q01217
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