› 6gfy

X-ray diffraction
2.7Å resolution

pVHL:EloB:EloC in complex with modified VH032 containing (3R,4S)-3-fluoro-4-hydroxyproline (ligand 14a)

Released:
DOI: 10.2210/pdb6gfy/pdb
PDB entry 6gfy coloured by chain, front view.
PDB entry 6gfy coloured by chain, side view.
PDB entry 6gfy 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 trimer (preferred)
PDBe Complex ID:
PDB-CPX-154086 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Elongin-B Chains: A, D, G, J
Molecule details ›
Chains: A, D, G, J
Length: 104 amino acids
Theoretical weight: 11.96 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
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 Chains: B, E, H, K
Molecule details ›
Chains: B, E, H, K
Length: 97 amino acids
Theoretical weight: 10.97 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
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 Chains: C, F, I, L
Molecule details ›
Chains: C, F, I, L
Length: 162 amino acids
Theoretical weight: 18.81 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P40337 (Residues: 54-213; Coverage: 75%)
Gene name: VHL
Sequence domains:
Structure domains:

Ligands and Environments

1 bound ligand:
Ligand EXH 4 x EXH
1 modified residue:
Ligand CAS 12 x CAS

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I04-1
Spacegroup: P4122
Unit cell:
a: 94.115Å b: 94.115Å c: 367.972Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.202 0.199 0.258
Expression system: Escherichia coli BL21(DE3)

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Citations

27 review citations

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

1 mention without citation

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Yu et al. (2021)