› 4z97

X-ray diffraction
3Å resolution

Crystal structure of USP7 in complex with DNMT1(K1115Q)

Released:
DOI: 10.2210/pdb4z97/pdb
PDB entry 4z97 coloured by chain, front view.
PDB entry 4z97 coloured by chain, side view.
PDB entry 4z97 coloured by chain, top view.
Source organism: Homo sapiens
Entry authors: Zhang ZM, Song J

Function and Biology Details

Reactions catalysed: 
Thiol-dependent hydrolysis of ester, thioester, amide, peptide and isopeptide bonds formed by the C-terminal Gly of ubiquitin (a 76-residue protein attached to proteins as an intracellular targeting signal).
S-adenosyl-L-methionine + DNA = S-adenosyl-L-homocysteine + DNA containing 5-methylcytosine
Biochemical function:
  • not assigned
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-150713 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Ubiquitin carboxyl-terminal hydrolase 7 Chain: A
Molecule details ›
Chain: A
Length: 530 amino acids
Theoretical weight: 61.89 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q93009 (Residues: 560-1083; Coverage: 48%)
Gene names: HAUSP, USP7
Sequence domains:
DNA (cytosine-5)-methyltransferase 1 Chain: C
Molecule details ›
Chain: C
Length: 33 amino acids
Theoretical weight: 3.46 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P26358 (Residues: 1098-1129; Coverage: 2%)
Gene names: AIM, CXXC9, DNMT, DNMT1

Ligands and Environments

1 bound ligand:
Ligand GOL 1 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 5.0.1
Spacegroup: P3221
Unit cell:
a: 123.659Å b: 123.659Å c: 152.928Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.212 0.209 0.254
Expression system: Escherichia coli

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