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Crystal structure of DNMT3A add domain E545R mutant bound to H3T3PH peptide

Analyse Crystal structure of DNMT3A add domain E545R mutant bound to H3T3PH peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB
4QBS
Type
protein
Length
145 residues
Chains
2
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
DNA (cytosine-5)-methyltransferase 3A; Histone H3
EC
2.1.1.37
UniProt
Q9Y6K1
Ligands
ZN, SO4

Structure

x-ray diffraction · 2 distinct chains · 30% helix, 18% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
ADNA (cytosine-5)-methyltransferase 3A (EC 2.1.1.37)protein13832% helix, 17% strandQ9Y6K1
PHistone H3protein70% helix, 43% strand—

Ligands and binding sites

  • ZN · Zinc ion · metal · 3 copies · chains A
  • SO4 · Sulfate ion · ion · chains A

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

Interfaces

1 interface between chains.

  • A–P · 548 Ų buried · 16 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 modified (phosphorylation).

Compared structures

  • 4QBS · Crystal structure of DNMT3a ADD domain E545R mutant bound to H3T3ph peptide · the same entry in another collection · chain A against A, TM-score 1.00
  • Q9Y6K1 · AlphaFold monomer V2.0 prediction for DNA (cytosine-5)-methyltransferase 3A (Q9Y6K1) · a predicted model of the same protein · chain A against A, TM-score 0.98

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