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Crystal structure of aminoglycoside 6'-acetyltransferase-ie

Analyse Crystal structure of aminoglycoside 6'-acetyltransferase-ie in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4QC6
Type: protein
Length: 358 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Bifunctional AAC/APH
EC: 2.3.1.-, 2.7.1.-
UniProt: Q7ATH7
Ligands: KAN, 30N
Pockets: 3 · best druggability 0.76

Structure

x-ray diffraction · 1 distinct chain · 32% helix, 35% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Bifunctional AAC/APH (EC 2.3.1.-, 2.7.1.-)	protein	179	32% helix, 35% strand	Q7ATH7

Ligands and binding sites

KAN · Kanamycin A · ligand · 2 copies · chains A, B
30N · (3R,5S,9R)-1-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]-3,5,9-trihydroxy-8,8-dimethyl-10,14-dioxo-2,4,6-trioxa-11,15-diaza-3,5-diphosphaheptadecane-17-sulfinic acid 3,5-dioxide (non-preferred name) · ligand · 2 copies · chains A, B
FMT · Formic acid · additive · 5 copies · chains A, B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	536	0.76	0.83	53	KAN, 30N, FMT
2	530	0.76	0.83	54	KAN, 30N, FMT
3	395	0.71	0.82	49	empty

Interfaces

1 interface between chains.

A–B · 370 Å² buried · 5 hydrogen bonds · protein-protein

Compared structures

4QC6 · Crystal structure of aminoglycoside 6'-acetyltransferase-Ie · the same entry in another collection · chain B against B, TM-score 1.00
Q7ATH7 · AlphaFold monomer V2.0 prediction for bifunctional AAC/APH (Q7ATH7) · 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 Q7ATH7
Elsewhere: RCSB PDB 4QC6 · PDBe 4QC6 · UniProt Q7ATH7

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