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: 16.47 kDa 
• Atom Count: 1,282 
• Modelled Residue Count: 129 
• Deposited Residue Count: 129 
• Unique protein chains: 1

 4YEM

Carboplatin binding to HEWL in NaBr crystallisation conditions studied at an X-ray wavelength of 0.9163A - new refinement

• PDB DOI: 10.2210/pdb4YEM/pdb

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


• Deposited: 2015-02-24 Released: 2015-03-04 
• Deposition Author(s): Shabalin, I.G., Dauter, Z., Jaskolski, M., Minor, W., Wlodawer, A.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.47 Å
• R-Value Free: 0.156 
• R-Value Work: 0.105 
• R-Value Observed: 0.108 

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 4XAN

Literature

Crystallography and chemistry should always go together: a cautionary tale of protein complexes with cisplatin and carboplatin.

Shabalin, I., Dauter, Z., Jaskolski, M., Minor, W., Wlodawer, A.

(2015) Acta Crystallogr D Biol Crystallogr 71: 1965-1979

• PubMed: 26327386 
• DOI: 10.1107/S139900471500629X
• Primary Citation of Related Structures:  
  4YDX, 4YEA, 4YEM, 4YEN, 4YEO


• PubMed Abstract: 
  

The anticancer activity of platinum-containing drugs such as cisplatin and carboplatin is considered to primarily arise from their interactions with nucleic acids; nevertheless, these drugs, or the products of their hydrolysis, also bind to proteins, potentially leading to the known side effects of the treatments. Here, over 40 crystal structures deposited in the Protein Data Bank (PDB) of cisplatin and carboplatin complexes of several proteins were analysed. Significant problems of either a crystallographic or a chemical nature were found in most of the presented atomic models and they could be traced to less or more serious deficiencies in the data-collection and refinement procedures. The re-evaluation of these data and models was possible thanks to their mandatory or voluntary deposition in publicly available databases, emphasizing the point that the availability of such data is critical for making structural science reproducible. Based on this analysis of a selected group of macromolecular structures, the importance of deposition of raw diffraction data is stressed and a procedure for depositing, tracking and using re-refined crystallographic models is suggested.

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Related Citations: 

• 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

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Organizational Affiliation: 

Protein Structure Section, MCL, National Cancer Institute, Frederick, MD 21702, USA.

Macromolecules

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
UniProt
Find proteins for P00698 (Gallus gallus) Explore P00698  Go to UniProtKB:  P00698

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PT	B [auth A], S [auth A], Y [auth A]	PLATINUM (II) ION Pt HRGDZIGMBDGFTC-UHFFFAOYSA-N
BR	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], 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]	BROMIDE ION Br CPELXLSAUQHCOX-UHFFFAOYSA-M
DMS	U [auth A], V [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
ACT	W [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
CL	X [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	T [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.47 Å
• R-Value Free: 0.156 
• R-Value Work: 0.105 
• R-Value Observed: 0.108 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.58	α = 90
b = 78.58	β = 90
c = 37.29	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
xia2	data reduction
MOSFLM	data reduction
Aimless	data scaling
Coot	model building
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2015-03-04 
Deposition Author(s): Shabalin, I.G., Dauter, Z., Jaskolski, M., Minor, W., Wlodawer, A.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	--

Revision History  

• Version 1.0: 2015-03-04
  Type: Initial release
  
• Version 1.1: 2015-09-09
  Changes: Database references
• Version 1.2: 2015-09-16
  Changes: Data collection
• Version 1.3: 2015-09-30
  Changes: Data collection
• Version 1.4: 2015-11-04
  Changes: Database references
• Version 1.5: 2017-09-06
  Changes: Author supporting evidence, Data collection, Derived calculations
• Version 1.6: 2019-12-25
  Changes: Author supporting evidence
• Version 1.7: 2022-04-13
  Changes: Database references, Structure summary