› 6gmq

X-ray diffraction
2.76Å resolution

pVHL:EloB:EloC in complex with (4-(1H-pyrrol-1-yl)phenyl)methanol

Released:
DOI: 10.2210/pdb6gmq/pdb
PDB entry 6gmq coloured by chain, front view.
PDB entry 6gmq coloured by chain, side view.
PDB entry 6gmq coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Surface Probing by Fragment-Based Screening and Computational Methods Identifies Ligandable Pockets on the von Hippel-Lindau (VHL) E3 Ubiquitin Ligase.
Lucas X, Van Molle I, Ciulli A
J Med Chem 61 7387-7393 (2018)
PMID: 30040896

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:
4 distinct polypeptide molecules
Macromolecules (4 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
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
Molecule details ›
Chains: B, E
Length: 97 amino acids
Theoretical weight: 11.08 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q15369 (Residues: 17-111; Coverage: 85%)
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
UniProt:
  • Canonical: P40337 (Residues: 54-213; Coverage: 75%)
Gene name: VHL
Sequence domains:
Structure domains:
Elongin-C Chains: H, K
Molecule details ›
Chains: H, K
Length: 97 amino acids
Theoretical weight: 10.97 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
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

Ligands and Environments

3 bound ligands:
Ligand ACT 3 x ACT
Ligand F4K 2 x F4K
Ligand IPA 2 x IPA
1 modified residue:
Ligand CAS 14 x CAS

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I24
Spacegroup: P4122
Unit cell:
a: 93.83Å b: 93.83Å c: 363.82Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.209 0.205 0.279
Expression system: Escherichia coli

Quick links

Citations

6 review citations

E3 Ligase Ligands for PROTACs: How They Were Found and How to Discover New Ones.
Ishida et al. (2021)
5 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