› 5m9n

X-ray diffraction
1.95Å resolution

Crystal structure of human TDRD1 extended Tudor domain in complex with a symmetrically dimethylated E2F peptide

Released:
DOI: 10.2210/pdb5m9n/pdb
PDB entry 5m9n coloured by chain, front view.
PDB entry 5m9n coloured by chain, side view.
PDB entry 5m9n coloured by chain, top view.
Source organism: Homo sapiens
Entry authors: Tallant C, Savitsky P, Moehlenbrink J, Chan C, Nunez-Alonso G, Newman JA, von Delft F, Arrowsmith CH, Edwards AM, Bountra C, Fedorov O, La Thangue NB, Knapp S, Structural Genomics Consortium (SGC)

Function and Biology Details

Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assemblies composition:
hetero dimer (preferred)
monomeric
Assembly name:
PDBe Complex ID:
PDB-CPX-169518 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Tudor domain-containing protein 1 Chains: A, B
Molecule details ›
Chains: A, B
Length: 220 amino acids
Theoretical weight: 24.31 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9BXT4 (Residues: 460-679; Coverage: 19%)
Gene name: TDRD1
Sequence domains: Tudor domain
Transcription factor E2F1 Chain: C
Molecule details ›
Chain: C
Length: 17 amino acids
Theoretical weight: 1.76 KDa
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: Q01094 (Residues: 104-120; Coverage: 4%)
Gene names: E2F1, RBBP3

Ligands and Environments

2 bound ligands:
Ligand EDO 3 x EDO
Ligand 2MR 1 x 2MR
1 modified residue:
Ligand 2MR 2 x 2MR

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I04
Spacegroup: P1
Unit cell:
a: 42.91Å b: 52.962Å c: 59.619Å
α: 64.94° β: 88.85° γ: 67.67°
R-values:
R R work R free
0.215 0.212 0.26
Expression systems:
  • Escherichia coli
  • Not provided

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