› 1yp7

X-ray diffraction
2Å resolution

Van der Waals Interactions Dominate Hydrophobic Association in a Protein Binding Site Occluded From Solvent Water

Released:
DOI: 10.2210/pdb1yp7/pdb
PDB entry 1yp7 coloured by chain, front view.
PDB entry 1yp7 coloured by chain, side view.
PDB entry 1yp7 coloured by chain, top view.
Source organism: Mus musculus
Primary publication:
Van der Waals interactions dominate ligand-protein association in a protein binding site occluded from solvent water.
Barratt E, Bingham RJ, Warner DJ, Laughton CA, Phillips SE, Homans SW
J Am Chem Soc 127 11827-34 (2005)
PMID: 16104761

Function and Biology Details

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

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-145879 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Major urinary protein 1 Chain: A
Molecule details ›
Chain: A
Length: 174 amino acids
Theoretical weight: 20.12 KDa
Source organism: Mus musculus
Expression system: Escherichia coli
UniProt:
  • Canonical: P11588 (Residues: 19-180; Coverage: 100%)
Gene name: Mup1
Sequence domains: Lipocalin / cytosolic fatty-acid binding protein family
Structure domains: Lipocalin

Ligands and Environments

1 bound ligand:
Ligand CD 3 x CD
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU
Spacegroup: P43212
Unit cell:
a: 56.459Å b: 56.459Å c: 104.071Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.198 0.197 0.256
Expression system: Escherichia coli

Quick links

Citations

10 review citations

Efficient incorporation of protein flexibility and dynamics into molecular docking simulations.
Lill MA. (2011)
9 more