› 8bb3

X-ray diffraction
1.8Å resolution

Structure of human WDR5 and pVHL:ElonginC:ElonginB bound to PROTAC with PEG linker (conformation #1)

Released:
DOI: 10.2210/pdb8bb3/pdb
PDB entry 8bb3 coloured by chain, front view.
PDB entry 8bb3 coloured by chain, side view.
PDB entry 8bb3 coloured by chain, top view.
Source organism: Homo sapiens
Entry authors: Kraemer A, Doelle A, Knapp S, Structural Genomics Consortium (SGC)

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
PDBe Complex ID:
PDB-CPX-154080 (preferred)
Entry contents:
4 distinct polypeptide molecules
Macromolecules (4 distinct):
Elongin-B Chain: J
Molecule details ›
Chain: 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 Chain: K
Molecule details ›
Chain: K
Length: 98 amino acids
Theoretical weight: 11.04 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q15369 (Residues: 16-112; Coverage: 87%)
Gene names: ELOC, TCEB1
Sequence domains: Skp1 family, tetramerisation domain
von Hippel-Lindau disease tumor suppressor Chain: L
Molecule details ›
Chain: L
Length: 162 amino acids
Theoretical weight: 18.7 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P40337 (Residues: 54-213; Coverage: 75%)
Gene name: VHL
Sequence domains:
WD repeat-containing protein 5 Chain: B
Molecule details ›
Chain: B
Length: 321 amino acids
Theoretical weight: 35.3 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P61964 (Residues: 33-334; Coverage: 90%)
Gene names: BIG3, WDR5
Sequence domains: WD domain, G-beta repeat

Ligands and Environments

4 bound ligands:
Ligand SCN 15 x SCN
Ligand EDO 13 x EDO
Ligand P6G 1 x P6G
Ligand Q3X 1 x Q3X
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X06DA
Spacegroup: P21
Unit cell:
a: 47.572Å b: 189.858Å c: 49.723Å
α: 90° β: 117.64° γ: 90°
R-values:
R R work R free
0.194 0.193 0.227
Expression system: Escherichia coli

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