PDBe 3dvn

X-ray diffraction
2.7Å resolution

Crystal structure of K63-specific fab Apu2.16 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 Chains: A, L
Molecule details ›
Chains: A, L
Length: 217 amino acids
Theoretical weight: 23.66 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 Chains: B, H
Molecule details ›
Chains: B, H
Length: 230 amino acids
Theoretical weight: 24.58 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
Structure domains: Immunoglobulins
Ubiquitin Chains: U, X
Molecule details ›
Chains: U, 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 Chains: V, Y
Molecule details ›
Chains: V, 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 BL11-1
Spacegroup: C2
Unit cell:
a: 177.705Å b: 94.571Å c: 97.74Å
α: 90° β: 107.21° γ: 90°
R-values:
R R work R free
0.223 0.22 0.268
Expression system: Escherichia coli