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Crystal structure of meta-AAC0038, an environmental aminoglycoside resistance enzyme, H168A mutant in complex with acetyl-CoA
Analyse Crystal structure of meta-AAC0038, an environmental aminoglycoside resistance… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6MN0
- Type
- protein
- Length
- 1,562 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aminoglycoside N(3)-acetyltransferase
- EC
- 2.3.1.81
- UniProt
- A0A059X981
- Ligands
- ACO, SO4, CL
- Pockets
- 16 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 37% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, E | Aminoglycoside N(3)-acetyltransferase (EC 2.3.1.81) | protein | 260 | 37% helix, 23% strand | A0A059X981 |
| C | Aminoglycoside N(3)-acetyltransferase (EC 2.3.1.81) | protein | 261 | 39% helix, 23% strand | A0A059X981 |
| D | Aminoglycoside N(3)-acetyltransferase (EC 2.3.1.81) | protein | 260 | 37% helix, 22% strand | A0A059X981 |
| F | Aminoglycoside N(3)-acetyltransferase (EC 2.3.1.81) | protein | 261 | 36% helix, 23% strand | A0A059X981 |
Ligands and binding sites
- ACO · Acetyl coenzyme *A · ligand · 6 copies · chains A, B, C, F, D, E
- SO4 · Sulfate ion · ion · 21 copies · chains A, B, C, D, E, F
- CL · Chloride ion · ion · 3 copies · chains A, C, F
- PE3 · 3,6,9,12,15,18,21,24,27,30,33,36,39-tridecaoxahentetracontane-1,41-diol · additive · 8 copies · chains A, C, D, B, E, F
- GOL · Glycerol · additive · 5 copies · chains A, D, B, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1170 | 0.86 | 0.87 | 150 | PE3 |
| 2 | 766 | 0.78 | 0.82 | 92 | CL |
| 3 | 554 | 0.71 | 0.80 | 64 | ACO |
| 4 | 488 | 0.65 | 0.77 | 62 | GOL |
| 5 | 430 | 0.65 | 0.78 | 53 | empty |
Interfaces
8 interfaces between chains.
- A–B · 983 Ų buried · 8 hydrogen bonds · protein-protein
- D–E · 954 Ų buried · 12 hydrogen bonds · protein-protein
- C–F · 874 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 476 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 448 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6MN0 · Crystal structure of meta-AAC0038, an environmental aminoglycoside resistance enzyme… · 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 A0A059X981
- Elsewhere: RCSB PDB 6MN0 · PDBe 6MN0 · UniProt A0A059X981
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