Research workbench
Crystal structure of acetylglutamate kinase from mycobacterium tuberculosis CDC1551
Analyse Crystal structure of acetylglutamate kinase from mycobacterium tuberculosis… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2AP9
- Type
- protein
- Length
- 1,762 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acetylglutamate kinase
- EC
- 2.7.2.8
- UniProt
- P0A4Y6
- Ligands
- MG, NI
- Pockets
- 20 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 40% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Acetylglutamate kinase (EC 2.7.2.8) | protein | 299 | 43% helix, 23% strand | P0A4Y6 |
| B, C, D, F | Acetylglutamate kinase (EC 2.7.2.8) | protein | 292 | 39% helix, 21% strand | P0A4Y6 |
| E | Acetylglutamate kinase (EC 2.7.2.8) | protein | 295 | 38% helix, 20% strand | P0A4Y6 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 180 | 0.69 | 0.87 | 22 | empty |
| 2 | 193 | 0.66 | 0.84 | 22 | empty |
| 3 | 210 | 0.65 | 0.83 | 22 | empty |
| 4 | 523 | 0.64 | 0.76 | 49 | empty |
| 5 | 431 | 0.63 | 0.77 | 40 | empty |
Interfaces
6 interfaces between chains.
- A–C · 1539 Ų buried · 7 hydrogen bonds · protein-protein
- D–F · 1503 Ų buried · 6 hydrogen bonds · protein-protein
- B–E · 1502 Ų buried · 9 hydrogen bonds · protein-protein
- A–F · 1343 Ų buried · 23 hydrogen bonds · protein-protein
- B–C · 1323 Ų buried · 25 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 42 modified (engineered).
Compared structures
- 2AP9 · Crystal structure of acetylglutamate kinase from Mycobacterium tuberculosis CDC1551 · the same entry in another collection · chain A against A, TM-score 1.00
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 P0A4Y6
- Elsewhere: RCSB PDB 2AP9 · PDBe 2AP9 · UniProt P0A4Y6
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