4G4H

100K X-ray diffraction study of carboplatin binding to HEWL in DMSO media after 13 months of crystal storage

DOI: 10.2210/pdb4G4H/pdb

Classification: HYDROLASE
Organism(s): Gallus gallus
Mutation(s): No

Deposited: 2012-07-16 Released: 2012-11-07
Deposition Author(s): Tanley, S.W.M., Schreurs, A.M.M., Kroon-Batenburg, L.M.J., Helliwell, J.R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.268
R-Value Work: 0.205
R-Value Observed: 0.208

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Room-temperature X-ray diffraction studies of cisplatin and carboplatin binding to His15 of HEWL after prolonged chemical exposure.

Tanley, S.W., Schreurs, A.M., Kroon-Batenburg, L.M., Helliwell, J.R.

(2012) Acta Crystallogr Sect F Struct Biol Cryst Commun 68: 1300-1306

PubMed: 23143236 Search on PubMedSearch on PubMed Central
DOI: 10.1107/S1744309112042005
Primary Citation of Related Structures:
4G49, 4G4B, 4G4C, 4G4H

PubMed Abstract:

The anticancer complexes cisplatin and carboplatin are known to bind to both the Nδ and the Nℇ atoms of His15 of hen egg-white lysozyme (HEWL) in the presence of dimethyl sulfoxide (DMSO). However, neither binds in aqueous media after 4 d of crystallization and crystal growth, suggesting that DMSO facilitates cisplatin/carboplatin binding to the N atoms of His15 by an unknown mechanism. Crystals of HEWL cocrystallized with cisplatin in both aqueous and DMSO media, of HEWL cocrystallized with carboplatin in DMSO medium and of HEWL cocrystallized with cisplatin and N-acetylglucosamine (NAG) in DMSO medium were stored for between seven and 15 months. X-ray diffraction studies of these crystals were carried out on a Bruker APEX II home-source diffractometer at room temperature. Room-temperature X-ray diffraction data collection removed the need for cryoprotectants to be used, ruling out any effect that the cryoprotectants might have had on binding to the protein. Both cisplatin and carboplatin still bind to both the Nδ and Nℇ atoms of His15 in DMSO media as expected, but more detail for the cyclobutanedicarboxylate (CBDC) moiety of carboplatin was observed at the Nℇ binding site. However, two molecules of cisplatin were now observed to be bound to His15 in aqueous conditions. The platinum peak positions were identified using anomalous difference electron-density maps as a cross-check with Fo-Fc OMIT electron-density maps. The occupancies of each binding site were calculated using SHELXTL. These results show that over time cisplatin binds to both N atoms of His15 of HEWL in aqueous media, whereas this binding is speeded up in the presence of DMSO. The implication of cisplatin binding to proteins after a prolonged period of time is an important consideration for the length of treatment in patients who are given cisplatin.

Organizational Affiliation:

School of Chemistry, Faculty of Engineering and Physical Sciences, University Of Manchester, Brunswick Street, Manchester M13 9PL, England.

Macromolecules

Find similar proteins by:

(by identity cutoff) | Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lysozyme C	A	129	Gallus gallus	Mutation(s): 0 Gene Names: LYZ EC: 3.2.1.17
Find proteins for P00698 (Gallus gallus) Explore P00698 Go to UniProtKB: P00698
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
QPT Query on QPT Download Ideal Coordinates CCD File SDF format, chain F [A] SDF format, chain G [A] MOL2 format, chain F [A] MOL2 format, chain G [A]	A	carboplatin C₆ H₁₂ N₂ O₄ Pt BHKICZDKIIDMNR-UHFFFAOYSA-L		Ligand Interaction
DMS Query on DMS Download Ideal Coordinates CCD File SDF format, chain B [A] SDF format, chain H [A] MOL2 format, chain B [A] MOL2 format, chain H [A]	A	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Ligand Interaction
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain C [A] SDF format, chain D [A] SDF format, chain E [A] MOL2 format, chain C [A] MOL2 format, chain D [A] MOL2 format, chain E [A]	A	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Ligand Interaction