Research workbench
Crystal structure of the amino acid kinase domain from saccharomyces cerevisiae acetylglutamate kinase without ligands
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
- 3ZZG
- Type
- protein
- Length
- 1,160 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
- Pockets
- 14 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | 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, 22% strand | Q01217 |
Pockets
14 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 638 | 0.72 | 0.79 | 53 | empty |
| 2 | 622 | 0.71 | 0.79 | 53 | empty |
| 3 | 541 | 0.70 | 0.79 | 50 | empty |
| 4 | 548 | 0.70 | 0.79 | 45 | empty |
| 5 | 295 | 0.67 | 0.82 | 39 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1105 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 1092 Ų buried · 17 hydrogen bonds · protein-protein
- A–D · 968 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 962 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 3ZZG · 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 0.92
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 3ZZG · PDBe 3ZZG · UniProt Q01217
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