MolNFT v1 · #182429 · protein

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

7MQK · Aminoglycoside N(3)-acetyltransferase III: “AAC(3)-iiia in complex with CoA and sisomicin”. X-ray diffraction, 2 ligands (SIS, COA), 12 pockets (best druggability 0.55). MolNFT v1 #182429 on GenesisL1: 3D structure, binding sites…

PDB: 7MQK
Type: protein
Length: 1,042 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: SIS, COA
Pockets: 12 · best druggability 0.55

Structure

x-ray diffraction · 2 distinct chains · 38% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Aminoglycoside N(3)-acetyltransferase III (EC 2.3.1.81)	protein	260	38% helix, 24% strand	P29808
B, D	Aminoglycoside N(3)-acetyltransferase III (EC 2.3.1.81)	protein	261	38% helix, 24% strand	P29808

Ligands and binding sites

SIS · (1S,2S,3R,4S,6R)-4,6-diamino-3-{[(2S,3R)-3-amino-6-(aminomethyl)-3,4-dihydro-2H-pyran-2-yl]oxy}-2-hydroxycyclohexyl 3-deoxy-4-C-methyl-3-(methylamino)-beta-L-arabinopyranoside · ligand · 4 copies · chains A, B, C, D
COA · Coenzyme A · ligand · 4 copies · chains A, B, C, D
GOL · Glycerol · additive · chains B

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

Pockets

12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	309	0.55	0.75	46	SIS
2	298	0.55	0.75	45	SIS
3	283	0.54	0.75	44	SIS
4	112	0.51	0.81	23	empty
5	211	0.48	0.75	32	SIS

Interfaces

5 interfaces between chains.

C–D · 689 Å² buried · 14 hydrogen bonds · protein-protein
A–B · 588 Å² buried · 12 hydrogen bonds · protein-protein
B–C · 441 Å² buried · 3 hydrogen bonds · protein-protein
A–D · 439 Å² buried · 3 hydrogen bonds · protein-protein
B–D · 57 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 4 modified (oxidation).

Compared structures

7MQK · AAC(3)-IIIa in complex with CoA and sisomicin · 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 C 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 7MQK · PDBe 7MQK · UniProt P29808

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