MolNFT v1 · #95217 · protein
Crystal structure of an acetate kinase from mycobacterium smegmatis bound to AMP and sulfate
4IJN: “Crystal structure of an acetate kinase from mycobacterium smegmatis bound to AMP and sulfate”. X-ray diffraction, 2 ligands (AMP, SO4), 10 pockets (best druggability 0.78). MolNFT v1 #95217 on GenesisL1: 3D structure, binding sites…
- 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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