› 3qht

X-ray diffraction
2.4Å resolution

Crystal Structure of the Monobody ySMB-1 bound to yeast SUMO

Released:
DOI: 10.2210/pdb3qht/pdb
PDB entry 3qht coloured by chain, front view.
PDB entry 3qht coloured by chain, side view.
PDB entry 3qht coloured by chain, top view.
Source organisms:
Primary publication:
Isoform-specific monobody inhibitors of small ubiquitin-related modifiers engineered using structure-guided library design.
Gilbreth RN, Truong K, Madu I, Koide A, Wojcik JB, Li NS, Piccirilli JA, Chen Y, Koide S
Proc Natl Acad Sci U S A 108 7751-6 (2011)
PMID: 21518904

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-163932 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Ubiquitin-like protein SMT3 Chains: A, B
Molecule details ›
Chains: A, B
Length: 98 amino acids
Theoretical weight: 11.2 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Escherichia coli
UniProt:
  • Canonical: Q12306 (Residues: 2-98; Coverage: 96%)
Gene names: D9719.15, SMT3, YDR510W
Sequence domains: Ubiquitin family
Structure domains: Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1
Monobody ySMB-1 Chains: C, D
Molecule details ›
Chains: C, D
Length: 97 amino acids
Theoretical weight: 10.39 KDa
Source organism: synthetic construct
Expression system: Escherichia coli
Structure domains: Immunoglobulins

Ligands and Environments

1 bound ligand:
Ligand GOL 8 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 21-ID-F
Spacegroup: P21212
Unit cell:
a: 59.637Å b: 175.462Å c: 52.83Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.226 0.223 0.272
Expression system: Escherichia coli

Quick links

Citations

5 review citations

Ubiquitin-like proteins.
van der Veen et al. (2012)
4 more

4 mentions without citation

Structural insights for engineering binding proteins based on non-antibody scaffolds.
Gilbreth et al. (2012)
3 more