PDBe 4u9w

X-ray diffraction
2.49Å resolution

Crystal Structure of NatD bound to H4/H2A peptide and CoA


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:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
N-alpha-acetyltransferase 40 Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 207 amino acids
Theoretical weight: 23.97 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt: Gene names: NAA40, NAT11, PATT1
Sequence domains: Acetyltransferase (GNAT) family
Histone H4 Chains: E, F, G, H
Molecule details ›
Chains: E, F, G, H
Length: 6 amino acids
Theoretical weight: 504 Da
Source organism: Homo sapiens
Expression system: Not provided
  • Canonical: NEW P62805 (Residues: 2-6; Coverage: 5%)
Gene names: H4/A, H4/B, H4/C, H4/D, H4/E, H4/G, H4/H, H4/I, H4/J, H4/K, H4/M, H4/N, H4/O, H4F2, H4FA, H4FB, H4FC, H4FD, H4FE, H4FG, H4FH, H4FI, H4FJ, H4FK, H4FM, H4FN, H4FO, HIST1H4A, HIST1H4B, HIST1H4C, HIST1H4D, HIST1H4E, HIST1H4F, HIST1H4H, HIST1H4I, HIST1H4J, HIST1H4K, HIST1H4L, HIST2H4, HIST2H4A, HIST2H4B, HIST4H4

Ligands and Environments

Cofactor: Ligand COA 4 x COA
2 bound ligands:

No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU MICROMAX-007 HF
Spacegroup: P21
Unit cell:
a: 52.901Å b: 93.288Å c: 100.329Å
α: 90° β: 96.69° γ: 90°
R R work R free
0.178 0.176 0.223
Expression systems:
  • Escherichia coli
  • Not provided