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Crystal structure of aminoglycoside acetyltransferase AAC(3)-iva, H154A mutant, in complex with apramycin
Analyse Crystal structure of aminoglycoside acetyltransferase AAC(3)-iva, H154A mutant… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6MN4
- Type
- protein
- Length
- 1,532 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aminoglycoside N(3)-acetyltransferase, AAC(3)-iva
- EC
- 2.3.1.81
- UniProt
- Q306W4
- Ligands
- AM2, ZN, PO4
- Pockets
- 15 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E | Aminoglycoside N(3)-acetyltransferase, AAC(3)-iva (EC 2.3.1.81) | protein | 258 | 37% helix, 22% strand | Q306W4 |
| F | Aminoglycoside N(3)-acetyltransferase, AAC(3)-iva (EC 2.3.1.81) | protein | 242 | 31% helix, 19% strand | Q306W4 |
Ligands and binding sites
- AM2 · Apramycin · ligand · 6 copies · chains A, B, C, D, E, F
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
- PO4 · Phosphate ion · ion · 6 copies · chains A, B, C, D, E, F
- EDO · 1,2-ethanediol · additive · 6 copies · chains A, B, E
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 6 copies · chains A, B, C, F, D, E
- GOL · Glycerol · additive · 2 copies · chains D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 956 | 0.73 | 0.77 | 110 | AM2, PO4 |
| 2 | 641 | 0.69 | 0.78 | 76 | PO4 |
| 3 | 208 | 0.65 | 0.83 | 34 | empty |
| 4 | 321 | 0.61 | 0.78 | 36 | empty |
| 5 | 313 | 0.60 | 0.78 | 31 | AM2 |
Interfaces
7 interfaces between chains.
- A–D · 763 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 720 Ų buried · 8 hydrogen bonds · protein-protein
- D–E · 611 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 586 Ų buried · 10 hydrogen bonds · protein-protein
- C–F · 585 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 6MN4 · Crystal structure of aminoglycoside acetyltransferase AAC(3)-IVa, H154A mutant, in… · 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 Q306W4
- Elsewhere: RCSB PDB 6MN4 · PDBe 6MN4 · UniProt Q306W4
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