› 5h1v

X-ray diffraction
2Å resolution

Complex structure of TRIM24 PHD-bromodomain and inhibitor 6

Released:
DOI: 10.2210/pdb5h1v/pdb
PDB entry 5h1v coloured by chain, front view.
PDB entry 5h1v coloured by chain, side view.
PDB entry 5h1v coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
The polar warhead of a TRIM24 bromodomain inhibitor rearranges a water-mediated interaction network.
Liu J, Li F, Bao H, Jiang Y, Zhang S, Ma R, Gao J, Wu J, Ruan K
FEBS J 284 1082-1095 (2017)
PMID: 28207202

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
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-127337 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Transcription intermediary factor 1-alpha Chains: A, B
Molecule details ›
Chains: A, B
Length: 183 amino acids
Theoretical weight: 21.23 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli 'BL21-Gold(DE3)pLysS AG'
UniProt:
  • Canonical: O15164 (Residues: 824-1006; Coverage: 17%)
Gene names: RNF82, TIF1, TIF1A, TRIM24
Sequence domains:
Structure domains:

Ligands and Environments

3 bound ligands:
Ligand ZN 4 x ZN
Ligand 7FU 2 x 7FU
Ligand DMS 1 x DMS
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL19U1
Spacegroup: P21
Unit cell:
a: 50.028Å b: 36.027Å c: 113.207Å
α: 90° β: 96.88° γ: 90°
R-values:
R R work R free
0.182 0.18 0.22
Expression system: Escherichia coli 'BL21-Gold(DE3)pLysS AG'

Quick links

Citations

3 review citations

Inhibitors of protein-protein interactions (PPIs): an analysis of scaffold choices and buried surface area.
Ran et al. (2018)
2 more

2 mentions without citation

E3 Ligases Meet Their Match: Fragment-Based Approaches to Discover New E3 Ligands and to Unravel E3 Biology.
Michaelides et al. (2023)
1 more