Research workbench
Crystal structure of aminoglycoside resistance enzyme ApmA, complex with kanamycin B and coenzyme A
Analyse Crystal structure of aminoglycoside resistance enzyme ApmA, complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7UUL
- Type
- protein
- Length
- 1,648 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.26
- Source
- Staphylococcus aureus
- Molecule
- Aminocyclitol acetyltransferase ApmA
- UniProt
- A0A1D0AST6
- Ligands
- 9CS, COA, SO4, CL
- Pockets
- 15 · best druggability 0.74
Structure
x-ray diffraction · resolution 2.26 · 5 distinct chains · 33% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Aminocyclitol acetyltransferase ApmA | protein | 274 | 32% helix, 21% strand | A0A1D0AST6 |
| B, F | Aminocyclitol acetyltransferase ApmA | protein | 275 | 33% helix, 21% strand | A0A1D0AST6 |
| C | Aminocyclitol acetyltransferase ApmA | protein | 273 | 33% helix, 21% strand | A0A1D0AST6 |
| D | Aminocyclitol acetyltransferase ApmA | protein | 275 | 33% helix, 21% strand | A0A1D0AST6 |
| E | Aminocyclitol acetyltransferase ApmA | protein | 276 | 33% helix, 21% strand | A0A1D0AST6 |
Ligands and binding sites
- 9CS · (1R,2S,3S,4R,6S)-4,6-diamino-3-[(3-amino-3-deoxy-alpha-D-glucopyranosyl)oxy]-2-hydroxycyclohexyl 2,6-diamino-2,6-dideoxy-alpha-D-glucopyranoside · ligand · 6 copies · chains A, B, D, C, F, E
- COA · Coenzyme A · ligand · 5 copies · chains A, B, D, C, F, E
- SO4 · Sulfate ion · ion · 9 copies · chains A, E, B, C, D, F
- CL · Chloride ion · ion · chains D
- EDO · 1,2-ethanediol · additive · 10 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 961 | 0.74 | 0.77 | 81 | 9CS, SO4, EDO |
| 2 | 718 | 0.72 | 0.79 | 72 | empty |
| 3 | 960 | 0.71 | 0.76 | 80 | 9CS |
| 4 | 668 | 0.64 | 0.74 | 62 | 9CS, SO4 |
| 5 | 494 | 0.64 | 0.76 | 57 | 9CS, COA |
Interfaces
9 interfaces between chains.
- C–F · 1712 Ų buried · 29 hydrogen bonds · protein-protein
- A–B · 1694 Ų buried · 28 hydrogen bonds · protein-protein
- B–D · 1686 Ų buried · 32 hydrogen bonds · protein-protein
- A–D · 1675 Ų buried · 28 hydrogen bonds · protein-protein
- B–F · 834 Ų buried · 11 hydrogen bonds · protein-protein
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 A0A1D0AST6
- Elsewhere: RCSB PDB 7UUL · PDBe 7UUL · UniProt A0A1D0AST6
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