4GCF | pdb_00004gcf

Room temperature X-ray diffraction study of a 6-fold molar excess of a cisplatin/carboplatin mixture binding to HEWL, Dataset 4

• PDB DOI: https://doi.org/10.2210/pdb4GCF/pdb

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


• Deposited: 2012-07-30 Released: 2013-01-02 
• Deposition Author(s): Helliwell, J.R., Tanley, S.W.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.50 Å
• R-Value Free: 
  0.235 (Depositor), 0.217 (DCC) 
• R-Value Work: 
  0.170 (Depositor), 0.168 (DCC) 
• R-Value Observed: 
  0.172 (Depositor) 

Starting Model: experimental

Literature

The crystal structure analysis of the relative binding of cisplatin and carboplatin in a mixture with histidine in a protein studied at 100 and 300 K with repeated X-ray irradiation.

Helliwell, J.R., Tanley, S.W.

(2013) Acta Crystallogr D Biol Crystallogr 69: 121-125

• PubMed: 23275170 
• DOI: https://doi.org/10.1107/S090744491204423X
• Primary Citation Related Structures: 
  4GCB, 4GCC, 4GCD, 4GCE, 4GCF


• PubMed Abstract: 
  

  The anticancer agents cisplatin and carboplatin bind to histidine in a protein. This crystal structure study at data-collection temperatures of 100 and 300 K examines their relative binding affinities to a histidine side chain and the effect of a high X-ray radiation dose of up to ∼1.8 MGy on the stability of the subsequent protein-Pt adducts. Cisplatin binding is visible at the histidine residue, but carboplatin binding is not. Five refined X-ray crystal structures are presented: one at 100 K as a reference and four at 300 K. The diffraction resolutions are 1.8, 2.0, 2.8, 2.9 and 3.5 Å.

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Organizational Affiliation: 
• School of Chemistry, University of Manchester, England, UK. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 14.8 kDa 
• Atom Count: 1,007 
• Modeled Residue Count: 129 
• Deposited Residue Count: 129 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lysozyme C	A	129	Gallus gallus	Mutation(s): 0  EC: 3.2.1.17
UniProt
Find proteins for P00698 (Gallus gallus) Explore P00698  Go to UniProtKB:  P00698

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PT	B [auth A], C [auth A]	PLATINUM (II) ION Pt HRGDZIGMBDGFTC-UHFFFAOYSA-N
DMS	D [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.50 Å
• R-Value Free:  0.235 (Depositor), 0.217 (DCC) 
• R-Value Work:  0.170 (Depositor), 0.168 (DCC) 
• R-Value Observed: 0.172 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.87	α = 90
b = 79.87	β = 90
c = 37.768	γ = 90

Software Package:

Software Name	Purpose
APEX	data collection
PHASER	phasing
REFMAC	refinement
APEX	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-01-02 
Deposition Author(s): Helliwell, J.R., Tanley, S.W.M.

Revision History  

• Version 1.0: 2013-01-02
  Type: Initial release
  
• Version 1.1: 2013-01-23
  Changes: Database references
• Version 1.2: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2024-10-30
  Changes: Structure summary