› 8wms

X-ray diffraction
2.4Å resolution

Crystal structure of human DPPA3 in complex with human UHRF1 PHD domain

Released:
DOI: 10.2210/pdb8wms/pdb
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PDB entry 8wms coloured by chain, front view.
PDB entry 8wms coloured by chain, side view.
PDB entry 8wms coloured by chain, top view.
Source organism: Homo sapiens
Entry authors: Shiraishi N, Arita K

Function and Biology Details

Reaction catalysed: 
S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine + [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + N(6)-ubiquitinyl-[acceptor protein]-L-lysine
Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-274925 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
E3 ubiquitin-protein ligase UHRF1 Chain: A
Molecule details ›
Chain: A
Length: 68 amino acids
Theoretical weight: 7.76 KDa
Source organism: Homo sapiens
Expression system: unidentified plasmid
UniProt:
  • Canonical: Q96T88 (Residues: 299-366; Coverage: 9%)
Gene names: ICBP90, NP95, RNF106, UHRF1
Sequence domains: PHD-finger
Developmental pluripotency-associated protein 3 Chain: B
Molecule details ›
Chain: B
Length: 38 amino acids
Theoretical weight: 4.56 KDa
Source organism: Homo sapiens
Expression system: unidentified plasmid
UniProt:
  • Canonical: Q6W0C5 (Residues: 81-118; Coverage: 24%)
Gene names: DPPA3, STELLAR

Ligands and Environments

1 bound ligand:
Ligand ZN 4 x ZN
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: PHOTON FACTORY BEAMLINE BL-17A
Spacegroup: I4122
Unit cell:
a: 77.802Å b: 77.802Å c: 140.674Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.235 0.233 0.266
Expression system: unidentified plasmid

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