4NSJ | pdb_00004nsj

Carboplatin binding to HEWL in 2M NH4formate, 0.1M HEPES at pH 7.5

• PDB DOI: https://doi.org/10.2210/pdb4NSJ/pdb

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


• Deposited: 2013-11-28 Released: 2014-10-15 
• Deposition Author(s): Tanley, S.W.M., Diederichs, K., Kroon-Batenburg, L.M.J., Levy, C., Schreurs, A.M.M., Helliwell, J.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.258 (Depositor), 0.265 (DCC) 
• R-Value Work: 
  0.199 (Depositor), 0.206 (DCC) 
• R-Value Observed: 
  0.202 (Depositor) 

Starting Model: experimental

Literature

Carboplatin binding to histidine.

Tanley, S.W., Diederichs, K., Kroon-Batenburg, L.M., Levy, C., Schreurs, A.M., Helliwell, J.R.

(2014) Acta Crystallogr F Struct Biol Commun 70: 1135-1142

• PubMed: 25195881 
• DOI: https://doi.org/10.1107/S2053230X14016161
• Primary Citation Related Structures: 
  4LT0, 4LT3, 4NSG, 4NSH, 4NSI, 4NSJ


• PubMed Abstract: 
  

  Carboplatin is a second-generation platinum anticancer agent used for the treatment of a variety of cancers. Previous X-ray crystallographic studies of carboplatin binding to histidine (in hen egg-white lysozyme; HEWL) showed the partial conversion of carboplatin to cisplatin owing to the high NaCl concentration used in the crystallization conditions. HEWL co-crystallizations with carboplatin in NaBr conditions have now been carried out to confirm whether carboplatin converts to the bromine form and whether this takes place in a similar way to the partial conversion of carboplatin to cisplatin observed previously in NaCl conditions. Here, it is reported that a partial chemical transformation takes place but to a transplatin form. Thus, to attempt to resolve purely carboplatin binding at histidine, this study utilized co-crystallization of HEWL with carboplatin without NaCl to eliminate the partial chemical conversion of carboplatin. Tetragonal HEWL crystals co-crystallized with carboplatin were successfully obtained in four different conditions, each at a different pH value. The structural results obtained show carboplatin bound to either one or both of the N atoms of His15 of HEWL, and this particular variation was dependent on the concentration of anions in the crystallization mixture and the elapsed time, as well as the pH used. The structural details of the bound carboplatin molecule also differed between them. Overall, the most detailed crystal structure showed the majority of the carboplatin atoms bound to the platinum centre; however, the four-carbon ring structure of the cyclobutanedicarboxylate moiety (CBDC) remained elusive. The potential impact of the results for the administration of carboplatin as an anticancer agent are described.

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Organizational Affiliation: 
• School of Chemistry, Faculty of Engineering and Physical Sciences, University of Manchester, Brunswick Street, Manchester M13 9PL, England.
Department of Biology, University of Konstanz, D-78457 Konstanz, Germany.
Crystal and Structural Chemistry, Bijvoet Center for Biomolecular Research, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands.
Manchester Institute of Biotechnology (MIB), University of Manchester, 131 Princess Street, Manchester M1 7DN, England.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 15.95 kDa 
• Atom Count: 1,136 
• 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 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
QPT	X [auth A]	carboplatin C6 H12 N2 O4 Pt BHKICZDKIIDMNR-UHFFFAOYSA-L
DMS	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
FMT	J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A], R [auth A], S [auth A], T [auth A], U [auth A], V [auth A]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N
NA	W [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.258 (Depositor), 0.265 (DCC) 
• R-Value Work:  0.199 (Depositor), 0.206 (DCC) 
• R-Value Observed: 0.202 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.496	α = 90
b = 77.496	β = 90
c = 37.123	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-10-15 
Deposition Author(s): Tanley, S.W.M., Diederichs, K., Kroon-Batenburg, L.M.J., Levy, C., Schreurs, A.M.M., Helliwell, J.R.

Revision History  

• Version 1.0: 2014-10-15
  Type: Initial release
  
• Version 1.1: 2018-03-07
  Changes: Advisory, Data collection
• Version 1.2: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2024-11-06
  Changes: Structure summary