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AAC(3)-iiia in complex with CoA and neomycin

Analyse AAC(3)-iiia in complex with CoA and neomycin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7MQL
Type: protein
Length: 1,043 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Aminoglycoside N(3)-acetyltransferase III
EC: 2.3.1.81
UniProt: P29808
Ligands: COA, RIO
Pockets: 13 · best druggability 0.52

Structure

x-ray diffraction · 2 distinct chains · 38% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, D	Aminoglycoside N(3)-acetyltransferase III (EC 2.3.1.81)	protein	261	38% helix, 23% strand	P29808
C	Aminoglycoside N(3)-acetyltransferase III (EC 2.3.1.81)	protein	260	38% helix, 22% strand	P29808

Ligands and binding sites

COA · Coenzyme A · ligand · 4 copies · chains A, B, C, D
RIO · Ribostamycin · ligand · 4 copies · chains A, B, C, D
FMT · Formic acid · additive · 8 copies · chains A, B, C, D

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

Pockets

13 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	274	0.52	0.75	46	RIO
2	133	0.51	0.80	26	empty
3	204	0.50	0.76	36	RIO
4	178	0.46	0.75	30	RIO
5	76	0.46	0.82	17	empty

Interfaces

5 interfaces between chains.

C–D · 672 Å² buried · 12 hydrogen bonds · protein-protein
A–B · 641 Å² buried · 15 hydrogen bonds · protein-protein
A–D · 417 Å² buried · 1 hydrogen bond · protein-protein
B–C · 413 Å² buried · 1 hydrogen bond · protein-protein
B–D · 56 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 4 modified (oxidation).

Compared structures

7MQL · AAC(3)-IIIa in complex with CoA and neomycin · the same entry in another collection · chain D against D, TM-score 1.00
P29808 · AlphaFold monomer V2.0 prediction for aminoglycoside N(3)-acetyltransferase III (P29808) · a predicted model of the same protein · chain D 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 P29808
Elsewhere: RCSB PDB 7MQL · PDBe 7MQL · UniProt P29808

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