4OWA

Carboplatin binding to HEWL under sodium iodide crystallisation conditions


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.796 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.184 

wwPDB Validation 3D Report Full Report


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Literature

Chemical conversion of cisplatin and carboplatin with histidine in a model protein crystallized under sodium iodide conditions.

Tanley, S.W.Helliwell, J.R.

(2014) Acta Crystallogr.,Sect.F 70: 1127-1131

  • DOI: 10.1107/S2053230X14013995
  • Primary Citation of Related Structures:  
  • Also Cited By: 5M1Y

  • PubMed Abstract: 
  • Cisplatin and carboplatin are platinum anticancer agents that are used to treat a variety of cancers. Previous X-ray crystallographic studies of carboplatin binding to histidine in hen egg-white lysozyme (HEWL) showed a partial chemical conversion of ...

    Cisplatin and carboplatin are platinum anticancer agents that are used to treat a variety of cancers. Previous X-ray crystallographic studies of carboplatin binding to histidine in hen egg-white lysozyme (HEWL) showed a partial chemical conversion of carboplatin to cisplatin owing to the high sodium chloride concentration used in the crystallization conditions. Also, the co-crystallization of HEWL with carboplatin in sodium bromide conditions resulted in the partial conversion of carboplatin to the transbromoplatin form, with a portion of the cyclobutanedicarboxylate (CBDC) moiety still present. The results of the co-crystallization of HEWL with cisplatin or carboplatin in sodium iodide conditions are now reported in order to determine whether the cisplatin and carboplatin converted to the iodo form, and whether this took place in a similar way to the partial conversion of carboplatin to cisplatin in NaCl conditions or to transbromoplatin in NaBr conditions as seen previously. It is reported here that a partial chemical transformation has taken place to a transplatin form for both ligands. The NaI-grown crystals belonged to the monoclinic space group P21 with two molecules in the asymmetric unit. The chemically transformed cisplatin and carboplatin bind to both His15 residues, i.e. in each asymmetric unit. The binding is only at the N(δ) atom of His15. A third platinum species is also seen in both conditions bound in a crevice between symmetry-related molecules. Here, the platinum is bound to three I atoms identified based on their anomalous difference electron densities and their refined occupancies, with the fourth bound atom being a Cl atom (in the cisplatin case) or a portion of the CBDC moiety (in the carboplatin case).


    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Lysozyme C
A, B
129Gallus gallusMutation(s): 0 
Gene Names: LYZ
EC: 3.2.1.17
Find proteins for P00698 (Gallus gallus)
Go to Gene View: LYZ
Go to UniProtKB:  P00698
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IOD
Query on IOD

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A, B
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
 Ligand Interaction
ACT
Query on ACT

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B
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
DMS
Query on DMS

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Download CCD File 
A, B
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
QPT
Query on QPT

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Download CCD File 
A, B
carboplatin
C6 H12 N2 O4 Pt
BHKICZDKIIDMNR-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.796 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.184 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 27.138α = 90.00
b = 62.561β = 92.59
c = 58.130γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
EPSRCUnited Kingdom--

Revision History 

  • Version 1.0: 2014-09-24
    Type: Initial release