› 4ddb

X-ray diffraction
3Å resolution

EVAL processed HEWL, cisplatin DMSO paratone pH 6.5

Released:
DOI: 10.2210/pdb4ddb/pdb
PDB entry 4ddb coloured by chain, front view.
PDB entry 4ddb coloured by chain, side view.
PDB entry 4ddb coloured by chain, top view.
Source organism: Gallus gallus
Primary publication:
Structural studies of the effect that dimethyl sulfoxide (DMSO) has on cisplatin and carboplatin binding to histidine in a protein.
Tanley SW, Schreurs AM, Kroon-Batenburg LM, Meredith J, Prendergast R, Walsh D, Bryant P, Levy C, Helliwell JR
Acta Crystallogr D Biol Crystallogr 68 601-12 (2012)
PMID: 22525758

Function and Biology Details

Reaction catalysed: 
Hydrolysis of (1->4)-beta-linkages between N-acetylmuramic acid and N-acetyl-D-glucosamine residues in a peptidoglycan and between N-acetyl-D-glucosamine residues in chitodextrins
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-132831 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Lysozyme C Chain: A
Molecule details ›
Chain: A
Length: 129 amino acids
Theoretical weight: 14.33 KDa
Source organism: Gallus gallus
UniProt:
  • Canonical: P00698 (Residues: 19-147; Coverage: 100%)
Gene name: LYZ
Sequence domains: C-type lysozyme/alpha-lactalbumin family
Structure domains: Lysozyme

Ligands and Environments

2 bound ligands:
Ligand CPT 2 x CPT
Ligand DMS 10 x DMS
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU MICROMAX-007
Spacegroup: P43212
Unit cell:
a: 79.641Å b: 79.641Å c: 37.018Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.217 0.214 0.28

Quick links

Citations

22 citation in other articles

Say no to DMSO: dimethylsulfoxide inactivates cisplatin, carboplatin, and other platinum complexes.
Hall et al. (2014)
21 more

5 mentions without citation

Error estimates in atom coordinates and B factors in macromolecular crystallography.
Helliwell JR. (2023)
4 more