PDBe 3dvg

X-ray diffraction
2.6Å resolution

Crystal structure of K63-specific fab Apu.3A8 bound to K63-linked di-ubiquitin

Released:

Function and Biology Details

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Entry contents:
4 distinct polypeptide molecules
Macromolecules (4 distinct):
IGK@ protein Chain: A
Molecule details ›
Chain: A
Length: 217 amino acids
Theoretical weight: 23.73 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q6PIL8 (Residues: 24-114, 115-236; Coverage: 98%)
Gene name: IGK@
Sequence domains:
Structure domains: Immunoglobulins
Human IgG1 fab fragment heavy chain Chain: B
Molecule details ›
Chain: B
Length: 230 amino acids
Theoretical weight: 24.59 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
Structure domains: Immunoglobulins
Ubiquitin Chain: X
Molecule details ›
Chain: X
Length: 80 amino acids
Theoretical weight: 8.97 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P0CG48 (Residues: 609-684; Coverage: 11%)
Gene name: UBC
Sequence domains: Ubiquitin family
Structure domains: Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1
Ubiquitin Chain: Y
Molecule details ›
Chain: Y
Length: 79 amino acids
Theoretical weight: 8.89 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P0CG48 (Residues: 609-684; Coverage: 11%)
Gene name: UBC
Sequence domains: Ubiquitin family
Structure domains: Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1

Ligands and Environments

No bound ligands

No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRL BEAMLINE BL7-1
Spacegroup: C2
Unit cell:
a: 106.806Å b: 88.117Å c: 90.226Å
α: 90° β: 108.28° γ: 90°
R-values:
R R work R free
0.224 0.219 0.261
Expression system: Escherichia coli