› 5m9o

X-ray diffraction
1.45Å resolution

Crystal structure of human SND1 extended Tudor domain in complex with a symmetrically dimethylated E2F peptide

Released:
DOI: 10.2210/pdb5m9o/pdb
PDB entry 5m9o coloured by chain, front view.
PDB entry 5m9o coloured by chain, side view.
PDB entry 5m9o coloured by chain, top view.
Source organism: Homo sapiens
Entry authors: Tallant C, Savitsky P, Moehlenbrink J, Chan C, Nunez-Alonso G, Siejka P, Sorrell FJ, von Delft F, Arrowsmith CH, Edwards AM, Bountra C, Fedorov O, La Thangue NB, Knapp S, Structural Genomics Consortium (SGC)

Function and Biology Details

Reaction catalysed: 
Endonucleolytic cleavage to nucleoside 3'-phosphates and 3'-phosphooligonucleotide end-products
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-169517 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Staphylococcal nuclease domain-containing protein 1 Chain: A
Molecule details ›
Chain: A
Length: 224 amino acids
Theoretical weight: 25.37 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q7KZF4 (Residues: 677-900; Coverage: 25%)
Gene names: SND1, TDRD11
Sequence domains:
Structure domains:
Transcription factor E2F1 Chain: B
Molecule details ›
Chain: B
Length: 9 amino acids
Theoretical weight: 1.02 KDa
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: Q01094 (Residues: 108-116; Coverage: 2%)
Gene names: E2F1, RBBP3

Ligands and Environments

No bound ligands
1 modified residue:
Ligand 2MR 2 x 2MR

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I04
Spacegroup: P21
Unit cell:
a: 36.243Å b: 80.626Å c: 39.289Å
α: 90° β: 90.38° γ: 90°
R-values:
R R work R free
0.23 0.229 0.261
Expression systems:
  • Escherichia coli
  • Not provided

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