› 3ztd

X-ray diffraction
2.79Å resolution

pVHL54-213-EloB-EloC complex _ methyl 4-(((2S,4R)-4-hydroxy-1-(2-(3- methylisoxazol-5-yl)acetyl)pyrrolidine-2-carboxamido)methyl)benzoate

Released:
DOI: 10.2210/pdb3ztd/pdb
PDB entry 3ztd coloured by chain, front view.
PDB entry 3ztd coloured by chain, side view.
PDB entry 3ztd coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Dissecting fragment-based lead discovery at the von Hippel-Lindau protein:hypoxia inducible factor 1α protein-protein interface.
Van Molle I, Thomann A, Buckley DL, So EC, Lang S, Crews CM, Ciulli A
Chem Biol 19 1300-12 (2012)
PMID: 23102223

Function and Biology Details

Biochemical function:
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: 118 amino acids
Theoretical weight: 13.15 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q15370 (Residues: 1-118; Coverage: 100%)
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: 18.7 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 ZTD 4 x ZTD
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID23-2
Spacegroup: P4122
Unit cell:
a: 94.081Å b: 94.081Å c: 366.494Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.229 0.224 0.309
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

44 review citations

Induced protein degradation: an emerging drug discovery paradigm.
Lai et al. (2017)
43 more

3 mentions without citation

Chemical modulation of transcription factors.
Wiedemann et al. (2018)
2 more