Research workbench
Crystal structure of a tetrameric acetylglutamate kinase from saccharomyces cerevisiae complexed with its substrate N- acetylglutamate
Analyse Crystal structure of a tetrameric acetylglutamate kinase from saccharomyces… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4AB7
- Type
- protein
- Length
- 3,381 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein ARG5,6, mitochondrial
- EC
- 1.2.1.38, 2.7.2.8
- UniProt
- Q01217
- Ligands
- NLG
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 40% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, E | Protein ARG5,6, mitochondrial (EC 1.2.1.38, 2.7.2.8) | protein | 405 | 39% helix, 26% strand | Q01217 |
| B, C, F, G | Protein ARG5,6, mitochondrial (EC 1.2.1.38, 2.7.2.8) | protein | 436 | 40% helix, 24% strand | Q01217 |
| H | Protein ARG5,6, mitochondrial (EC 1.2.1.38, 2.7.2.8) | protein | 422 | 41% helix, 24% strand | Q01217 |
Ligands and binding sites
- NLG · N-acetyl-L-glutamate · ligand · 2 copies · chains D, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 849 | 0.81 | 0.84 | 102 | empty |
| 2 | 635 | 0.74 | 0.81 | 80 | empty |
| 3 | 1176 | 0.74 | 0.77 | 91 | empty |
| 4 | 504 | 0.70 | 0.80 | 52 | NLG |
| 5 | 441 | 0.69 | 0.80 | 58 | empty |
Interfaces
15 interfaces between chains.
- F–G · 1709 Ų buried · 20 hydrogen bonds · protein-protein
- B–C · 1671 Ų buried · 17 hydrogen bonds · protein-protein
- A–E · 1197 Ų buried · 14 hydrogen bonds · protein-protein
- G–H · 1160 Ų buried · 25 hydrogen bonds · protein-protein
- C–D · 1154 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 4AB7 · Crystal structure of a tetrameric acetylglutamate kinase from Saccharomyces cerevisiae… · the same entry in another collection · chain H against H, TM-score 1.00
- Q01217 · AlphaFold monomer V2.0 prediction for protein ARG5,6, mitochondrial (Q01217) · a predicted model of the same protein · chain B against A, TM-score 0.96
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 4AB7 · PDBe 4AB7 · UniProt Q01217
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