› 6gfx

X-ray diffraction
1.83Å resolution

pVHL:EloB:EloC in complex with modified HIF-1a CODD peptide containing (3R,4S)-3-fluoro-4-hydroxyproline (ligand 13a)

Released:
DOI: 10.2210/pdb6gfx/pdb
PDB entry 6gfx coloured by chain, front view.
PDB entry 6gfx coloured by chain, side view.
PDB entry 6gfx coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
3-Fluoro-4-hydroxyprolines: Synthesis, Conformational Analysis, and Stereoselective Recognition by the VHL E3 Ubiquitin Ligase for Targeted Protein Degradation.
Testa A, Lucas X, Castro GV, Chan KH, Wright JE, Runcie AC, Gadd MS, Harrison WTA, Ko EJ, Fletcher D, Ciulli A
J Am Chem Soc 140 9299-9313 (2018)
PMID: 29949369

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-154087 (preferred)
Entry contents:
4 distinct polypeptide molecules
Macromolecules (4 distinct):
Elongin-B Chain: A
Molecule details ›
Chain: A
Length: 104 amino acids
Theoretical weight: 11.75 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: Q15370 (Residues: 1-104; Coverage: 88%)
Gene names: ELOB, TCEB2
Sequence domains: Ubiquitin family
Structure domains: Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1
Elongin-C Chain: B
Molecule details ›
Chain: B
Length: 97 amino acids
Theoretical weight: 10.97 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: Q15369 (Residues: 17-112; Coverage: 86%)
Gene names: ELOC, TCEB1
Sequence domains: Skp1 family, tetramerisation domain
Structure domains: Potassium Channel Kv1.1; Chain A
von Hippel-Lindau disease tumor suppressor Chain: C
Molecule details ›
Chain: C
Length: 160 amino acids
Theoretical weight: 18.56 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: P40337 (Residues: 54-213; Coverage: 75%)
Gene name: VHL
Sequence domains:
Structure domains:
Hypoxia-inducible factor 1-alpha Chain: D
Molecule details ›
Chain: D
Length: 19 amino acids
Theoretical weight: 2.26 KDa
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: Q16665 (Residues: 560-577; Coverage: 2%)
Gene names: BHLHE78, HIF1A, MOP1, PASD8
Sequence domains: Hypoxia-inducible factor-1

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I03
Spacegroup: P43212
Unit cell:
a: 59.258Å b: 59.258Å c: 245.337Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.185 0.183 0.212
Expression systems:
  • Escherichia coli BL21
  • Not provided

Quick links

Citations

26 review citations

PROteolysis TArgeting Chimeras (PROTACs) - Past, present and future.
Pettersson et al. (2019)
25 more

1 mention without citation

Discovery of small molecule ligands for the von Hippel-Lindau (VHL) E3 ligase and their use as inhibitors and PROTAC degraders.
Diehl et al. (2022)