› 2dm5

X-ray diffraction
1.7Å resolution

Thermodynamic Penalty Arising From Burial of a Ligand Polar Group Within a Hydrophobic Pocket of a Protein Receptor

Released:
DOI: 10.2210/pdb2dm5/pdb
PDB entry 2dm5 coloured by chain, front view.
PDB entry 2dm5 coloured by chain, side view.
PDB entry 2dm5 coloured by chain, top view.
Source organism: Mus musculus
Primary publication:
Thermodynamic penalty arising from burial of a ligand polar group within a hydrophobic pocket of a protein receptor.
Barratt E, Bronowska A, Vondrásek J, Cerný J, Bingham R, Phillips S, Homans SW
J Mol Biol 362 994-1003 (2006)
PMID: 16935302

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-145881 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Major urinary protein 2 Chain: A
Molecule details ›
Chain: A
Length: 174 amino acids
Theoretical weight: 20.14 KDa
Source organism: Mus musculus
Expression system: Escherichia coli
UniProt:
  • Canonical: P11589 (Residues: 19-180; Coverage: 100%)
Gene name: Mup2
Sequence domains: Lipocalin / cytosolic fatty-acid binding protein family
Structure domains: Lipocalin

Ligands and Environments

2 bound ligands:
Ligand CD 4 x CD
Ligand ODI 1 x ODI
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU RUH3R
Spacegroup: P43212
Unit cell:
a: 53.522Å b: 53.522Å c: 137.192Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.19 0.19 0.2
Expression system: Escherichia coli

Quick links

Citations

3 review citations

A medicinal chemist's guide to molecular interactions.
Bissantz et al. (2010)
2 more

1 mention without citation

R-hydroxynitrile lyase from the cyanogenic millipede, Chamberlinius hualienensis-A new entry to the carrier protein family Lipocalines.
Motojima et al. (2021)