› 7kd7

X-ray diffraction
1.44Å resolution

Crystal structure of human NatD (NAA40) bound to a bisubstrate analogue

Released:
DOI: 10.2210/pdb7kd7/pdb
PDB entry 7kd7 coloured by chain, front view.
PDB entry 7kd7 coloured by chain, side view.
PDB entry 7kd7 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Novel Bisubstrate Inhibitors for Protein N-Terminal Acetyltransferase D.
Deng Y, Deng S, Ho YH, Gardner SM, Huang Z, Marmorstein R, Huang R
J Med Chem 64 8263-8271 (2021)
PMID: 34110812

Function and Biology Details

Reaction catalysed: 
Acetyl-CoA + an N-terminal-L-seryl-[histone H2A] = an N-terminal-N(alpha)-acetyl-L-seryl-[histone H2A] + CoA
Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-168354 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
N-alpha-acetyltransferase 40 Chains: A, D
Molecule details ›
Chains: A, D
Length: 204 amino acids
Theoretical weight: 23.7 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli K-12
UniProt:
  • Canonical: Q86UY6 (Residues: 17-220; Coverage: 86%)
Gene names: NAA40, NAT11, PATT1
Sequence domains: Acetyltransferase (GNAT) family
SER-GLY-ARG-GLY-LYS Chains: B, E
Molecule details ›
Chains: B, E
Length: 5 amino acids
Theoretical weight: 506 Da
Source organism: Homo sapiens
Expression system: Not provided

Ligands and Environments


Cofactor: Ligand CMC 2 x CMC
4 bound ligands:
Ligand GOL 4 x GOL
Ligand SO4 4 x SO4
Ligand BTB 1 x BTB
Ligand NH2 2 x NH2
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 21-ID-E
Spacegroup: P212121
Unit cell:
a: 46.433Å b: 74.349Å c: 126.821Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.162 0.161 0.183
Expression systems:
  • Escherichia coli K-12
  • Not provided

Quick links

Citations

3 citation in other articles

Effects of Oncohistone Mutations and PTM Crosstalk on the N-Terminal Acetylation Activities of NatD.
Ho et al. (2023)
2 more

1 mention without citation

Novel Bisubstrate Inhibitors for Protein N-Terminal Acetyltransferase D.
Deng et al. (2021)