Research workbench
Crystal structure of an acetate kinase from mycobacterium smegmatis bound to AMP and sulfate
Analyse Crystal structure of an acetate kinase from mycobacterium smegmatis bound to… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4IJN
- Type
- protein
- Length
- 751 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acetate kinase
- EC
- 2.7.2.1
- UniProt
- A0QQK1
- Ligands
- AMP, SO4
- Pockets
- 10 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Acetate kinase (EC 2.7.2.1) | protein | 376 | 43% helix, 18% strand | A0QQK1 |
| B | Acetate kinase (EC 2.7.2.1) | protein | 375 | 44% helix, 18% strand | A0QQK1 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 106 | 0.78 | 0.98 | 29 | empty |
| 2 | 539 | 0.66 | 0.77 | 58 | SO4, AMP, EDO |
| 3 | 428 | 0.66 | 0.79 | 47 | SO4, AMP |
| 4 | 86 | 0.45 | 0.80 | 26 | empty |
| 5 | 73 | 0.41 | 0.80 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 3237 Ų buried · 31 hydrogen bonds · protein-protein
Compared structures
- 4IJN · Crystal structure of an acetate kinase from Mycobacterium smegmatis bound to AMP and… · the same entry in another collection · chain A against A, TM-score 1.00
- A0QQK1 · AlphaFold monomer V2.0 prediction for acetate kinase (A0QQK1) · 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 A0QQK1
- Elsewhere: RCSB PDB 4IJN · PDBe 4IJN · UniProt A0QQK1
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