› 6wfg

X-ray diffraction
2.16Å resolution

Crystal structure of human Naa50 in complex with an inhibitor (compound 3) identified using DNA encoded library technology

Released:
DOI: 10.2210/pdb6wfg/pdb
PDB entry 6wfg coloured by chain, front view.
PDB entry 6wfg coloured by chain, side view.
PDB entry 6wfg coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Characterization of Specific N-α-Acetyltransferase 50 (Naa50) Inhibitors Identified Using a DNA Encoded Library.
Kung PP, Bingham P, Burke BJ, Chen Q, Cheng X, Deng YL, Dou D, Feng J, Gallego GM, Gehring MR, Grant SK, Greasley S, Harris AR, Maegley KA, Meier J, Meng X, Montano JL, Morgan BA, Naughton BS, Palde PB, Paul TA, Richardson P, Sakata S, Shaginian A, Sonnenburg WK, Subramanyam C, Timofeevski S, Wan J, Yan W, Stewart AE
ACS Med Chem Lett 11 1175-1184 (2020)
PMID: 32550998

Function and Biology Details

Reaction catalysed: 
Acetyl-CoA + an N-terminal-L-methionyl-L-alanyl-[protein] = an N-terminal-N(alpha)-acetyl-L-methionyl-L-alanyl-[protein] + CoA
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-190462 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
N-alpha-acetyltransferase 50 Chains: A, C, E
Molecule details ›
Chains: A, C, E
Length: 171 amino acids
Theoretical weight: 19.57 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q9GZZ1 (Residues: 1-169; Coverage: 100%)
Gene names: MAK3, NAA50, NAT13, NAT5
Sequence domains: Acetyltransferase (GNAT) family

Ligands and Environments


Cofactor: Ligand COA 3 x COA
1 bound ligand:
Ligand U3V 3 x U3V
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 17-ID
Spacegroup: P21
Unit cell:
a: 47.83Å b: 102.94Å c: 67.64Å
α: 90° β: 106.71° γ: 90°
R-values:
R R work R free
0.203 0.201 0.253
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

5 review citations

DNA-Encoded Chemistry: Drug Discovery from a Few Good Reactions.
Fitzgerald et al. (2021)
4 more

1 mention without citation

Characterization of Specific N-α-Acetyltransferase 50 (Naa50) Inhibitors Identified Using a DNA Encoded Library.
Kung et al. (2020)