› 3n84

X-ray diffraction
2Å resolution

Crystal Structure of the Grb2 SH2 Domain in Complex with a 23-Membered Macrocyclic Ligand Having the Sequence pYVNVP

Released:
DOI: 10.2210/pdb3n84/pdb
PDB entry 3n84 coloured by chain, front view.
PDB entry 3n84 coloured by chain, side view.
PDB entry 3n84 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Thermodynamic and Structural Effects of Macrocyclization as a Constraining Method in Protein-Ligand Interactions.
Delorbe JE, Clements JH, Whiddon BB, Martin SF
ACS Med Chem Lett 1 448-452 (2010)
PMID: 21116482

Function and Biology Details

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

Structure analysis Details

Assemblies composition:
hetero tetramer (preferred)
hetero dimer
Assembly name:
PDBe Complex ID:
PDB-CPX-158881 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Growth factor receptor-bound protein 2 Chains: A, B, C, D, E, F
Molecule details ›
Chains: A, B, C, D, E, F
Length: 112 amino acids
Theoretical weight: 13.06 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
23-membered peptide-like macrocyclic ligand Chains: G, H, I, J, K, L
Molecule details ›
Chains: G, H, I, J, K, L
Length: 6 amino acids
Theoretical weight: 798 Da
Source organism: Homo sapiens
Expression system: Not provided

Ligands and Environments

3 bound ligands:
Ligand CL 2 x CL
Ligand GOL 7 x GOL
Ligand MG 1 x MG
1 modified residue:
Ligand PTR 6 x PTR

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU RU200
Spacegroup: C2
Unit cell:
a: 83.223Å b: 141.32Å c: 62.452Å
α: 90° β: 89.99° γ: 90°
R-values:
R R work R free
0.18 0.18 0.223
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

13 review citations

Counting on natural products for drug design.
Rodrigues et al. (2016)
12 more

3 mentions without citation

Thermodynamic and Structural Effects of Macrocyclization as a Constraining Method in Protein-Ligand Interactions.
Delorbe et al. (2010)
2 more