› 3u30

X-ray diffraction
2.43Å resolution

Crystal structure of a linear-specific Ubiquitin fab bound to linear ubiquitin

Released:
DOI: 10.2210/pdb3u30/pdb
PDB entry 3u30 coloured by chain, front view.
PDB entry 3u30 coloured by chain, side view.
PDB entry 3u30 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Engineering and structural characterization of a linear polyubiquitin-specific antibody.
Matsumoto ML, Dong KC, Yu C, Phu L, Gao X, Hannoush RN, Hymowitz SG, Kirkpatrick DS, Dixit VM, Kelley RF
J Mol Biol 418 134-44 (2012)
PMID: 22227388

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-209610 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Ubiquitin Chains: A, D
Molecule details ›
Chains: A, D
Length: 172 amino acids
Theoretical weight: 19.31 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P0CG48 (Residues: 533-684; Coverage: 22%)
Gene name: UBC
Sequence domains: Ubiquitin family
Structure domains: Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1
Light chain Fab Chains: B, E
Molecule details ›
Chains: B, E
Length: 214 amino acids
Theoretical weight: 23.33 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
Structure domains: Immunoglobulins
Heavy chain Fab Chains: C, F
Molecule details ›
Chains: C, F
Length: 227 amino acids
Theoretical weight: 24.04 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
Structure domains: Immunoglobulins

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 5.0.2
Spacegroup: P1
Unit cell:
a: 53.322Å b: 59.767Å c: 96.033Å
α: 87.08° β: 76.77° γ: 71.7°
R-values:
R R work R free
0.231 0.229 0.258
Expression system: Escherichia coli

Quick links

Citations

29 review citations

Ubiquitin modifications.
Swatek et al. (2016)
28 more

1 mention without citation

Performance of ZDOCK and IRAD in CAPRI rounds 28-34.
Vreven et al. (2017)