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Crystal structure of apo form of acetate kinase (acka) from salmonella typhimurium
Analyse Crystal structure of apo form of acetate kinase (acka) from salmonella… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3SLC
- Type
- protein
- Length
- 1,578 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acetate kinase
- EC
- 2.7.2.1
- UniProt
- P63411
- Pockets
- 12 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 41% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Acetate kinase (EC 2.7.2.1) | protein | 401 | 43% helix, 19% strand | P63411 |
| B, D | Acetate kinase (EC 2.7.2.1) | protein | 398 | 41% helix, 18% strand | P63411 |
| C | Acetate kinase (EC 2.7.2.1) | protein | 381 | 39% helix, 19% strand | P63411 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 152 | 0.80 | 0.97 | 31 | empty |
| 2 | 148 | 0.80 | 0.97 | 36 | empty |
| 3 | 703 | 0.68 | 0.76 | 93 | empty |
| 4 | 544 | 0.68 | 0.78 | 73 | EDO |
| 5 | 567 | 0.67 | 0.77 | 64 | empty |
Interfaces
3 interfaces between chains.
- C–D · 3188 Ų buried · 36 hydrogen bonds · protein-protein
- A–B · 3173 Ų buried · 31 hydrogen bonds · protein-protein
- A–C · 295 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 3SLC · Crystal structure of apo form of acetate kinase (AckA) from Salmonella typhimurium · the same entry in another collection · chain D against D, TM-score 1.00
- P63411 · AlphaFold monomer V2.0 prediction for acetate kinase acka (P63411) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 P63411
- Elsewhere: RCSB PDB 3SLC · PDBe 3SLC · UniProt P63411
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