› 3imd

X-ray diffraction
2Å resolution

Crystal Structure of the Grb2 SH2 Domain in Complex with a Flexible Ac-pY-Q-N-NH2 Tripeptide Mimic

Released:
DOI: 10.2210/pdb3imd/pdb
PDB entry 3imd coloured by chain, front view.
PDB entry 3imd coloured by chain, side view.
PDB entry 3imd coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Thermodynamic and structural effects of conformational constraints in protein-ligand interactions. Entropic paradoxy associated with ligand preorganization.
DeLorbe JE, Clements JH, Teresk MG, Benfield AP, Plake HR, Millspaugh LE, Martin SF
J Am Chem Soc 131 16758-70 (2009)
PMID: 19886660

Function and Biology Details

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

Structure analysis Details

Assemblies composition:
monomeric (preferred)
homo dimer
Assembly name:
PDBe Complex ID:
PDB-CPX-158852 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Growth factor receptor-bound protein 2 Chains: A, B
Molecule details ›
Chains: A, B
Length: 117 amino acids
Theoretical weight: 13.76 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P62993 (Residues: 53-163; Coverage: 51%)
Gene names: ASH, GRB2
Sequence domains: SH2 domain
Structure domains: SH2 domain

Ligands and Environments

3 bound ligands:
Ligand FYQ 2 x FYQ
Ligand CL 4 x CL
Ligand MG 1 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU RU200
Spacegroup: P212121
Unit cell:
a: 42.239Å b: 42.243Å c: 110.384Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.199 0.199 0.237
Expression system: Escherichia coli

Quick links

Citations

11 review citations

Advances in all atom sampling methods for modeling protein-ligand binding affinities.
Gallicchio et al. (2011)
10 more

4 mentions without citation

Binding of flexible and constrained ligands to the Grb2 SH2 domain: structural effects of ligand preorganization.
Clements et al. (2010)
3 more