› 6fmk

X-ray diffraction
2.75Å resolution

pVHL:EloB:EloC in complex with N-((S)-1-((2S,4R)-4-hydroxy-2-((4-(4-methylthiazol-5-yl)benzyl)carbamothioyl) pyrrolidin-1-yl)-1-thioxopropan-2-yl)acetamide (ligand 4)

Released:
DOI: 10.2210/pdb6fmk/pdb
PDB entry 6fmk coloured by chain, front view.
PDB entry 6fmk coloured by chain, side view.
PDB entry 6fmk coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Thioamide substitution to probe the hydroxyproline recognition of VHL ligands.
Soares P, Lucas X, Ciulli A
Bioorg Med Chem 26 2992-2995 (2018)
PMID: 29650462

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: 153 amino acids
Theoretical weight: 17.74 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P40337 (Residues: 54-204; Coverage: 71%)
Gene name: VHL
Sequence domains:
Structure domains:

Ligands and Environments

1 bound ligand:
Ligand DV8 4 x DV8
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: 94.768Å b: 94.768Å c: 365.819Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.199 0.196 0.26
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

1 review citation

PROteolysis TArgeting Chimeras (PROTACs) - Past, present and future.
Pettersson et al. (2019)
4 other articles

2 mentions 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)
1 more