› 9bju

X-ray diffraction
2.47Å resolution

Crystal structure of the complex between VHL, ElonginB, ElonginC, and compound 5

Released:
DOI: 10.2210/pdb9bju/pdb
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PDB entry 9bju coloured by chain, front view.
PDB entry 9bju coloured by chain, side view.
PDB entry 9bju coloured by chain, top view.
Source organisms:
Primary publication:
Potency-Enhanced Peptidomimetic VHL Ligands with Improved Oral Bioavailability.
Wu H, Murray J, Ishisoko N, Frommlet A, Deshmukh G, DiPasquale A, Mulvihill MM, Zhang D, Quinn JG, Blake RA, Fairbrother WJ, Fuhrmann J
J Med Chem 67 8585-8608 (2024)
PMID: 38809766

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
PDBe Complex ID:
PDB-CPX-279930 (preferred)
Entry contents:
5 distinct polypeptide molecules
Macromolecules (5 distinct):
Elongin-B Chains: A, D, G, J
Molecule details ›
Chains: A, D, G, J
Length: 104 amino acids
Theoretical weight: 11.75 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
Elongin-C Chains: B, E, H, K
Molecule details ›
Chains: B, E, H, K
Length: 96 amino acids
Theoretical weight: 10.84 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
von Hippel-Lindau disease tumor suppressor Chains: C, L
von Hippel-Lindau disease tumor suppressor Chains: F, I
3-PYRIDIN-4-YL-2,4-DIHYDRO-INDENO[1,2-.C.]PYRAZOLE Chains: W, X, Y, Z

Ligands and Environments

5 bound ligands:
Ligand TFA 2 x TFA
Ligand PEG 1 x PEG
Ligand EDO 2 x EDO
Ligand ACT 3 x ACT
Ligand DMS 3 x DMS
3 modified residues:
Ligand CSX 2 x CSX
Ligand TBG 4 x TBG
Ligand HYP 4 x HYP

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: SSRF BEAMLINE BL19U1
Spacegroup: P4122
Unit cell:
a: 93.297Å b: 93.297Å c: 362.757Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.22 0.218 0.256
Expression systems:
  • Escherichia coli
  • Not provided

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