Research workbench
Aminoglycoside N-2'-acetyltransferase-ia [AAC(2')-ia] in complex with acetylated-tobramycin and CoA
Analyse Aminoglycoside N-2'-acetyltransferase-ia [AAC(2')-ia] in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6VR2
- Type
- protein
- Length
- 353 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aminoglycoside 2'-N-acetyltransferase
- EC
- 2.3.1.59
- UniProt
- Q52424
- Ligands
- R7Y, COA
- Pockets
- 4 · best druggability 0.61
Structure
x-ray diffraction · 2 distinct chains · 28% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Aminoglycoside 2'-N-acetyltransferase (EC 2.3.1.59) | protein | 177 | 29% helix, 36% strand | Q52424 |
| B | Aminoglycoside 2'-N-acetyltransferase (EC 2.3.1.59) | protein | 176 | 28% helix, 36% strand | Q52424 |
Ligands and binding sites
- R7Y · (1S,2S,3R,4S,6R)-3-{[2-(acetylamino)-6-amino-2,3,6-trideoxy-alpha-D-ribo-hexopyranosyl]oxy}-4,6-diamino-2-hydroxycycloh exyl 3-amino-3-deoxy-alpha-D-glucopyranoside · ligand · 2 copies · chains A, B
- COA · Coenzyme A · ligand · 2 copies · chains A, B
- ACT · Acetate ion · additive · 7 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 367 | 0.61 | 0.77 | 33 | R7Y, COA |
| 2 | 326 | 0.60 | 0.78 | 34 | R7Y, COA |
| 3 | 118 | 0.49 | 0.80 | 24 | empty |
| 4 | 105 | 0.49 | 0.81 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 1127 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 6VR2 · Aminoglycoside N-2'-Acetyltransferase-Ia [AAC(2')-Ia] in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
- Q52424 · AlphaFold monomer V2.0 prediction for aminoglycoside 2'-N-acetyltransferase (Q52424) · 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 Q52424
- Elsewhere: RCSB PDB 6VR2 · PDBe 6VR2 · UniProt Q52424
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.