4YEM

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


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 

wwPDB Validation   3D Report Full Report


This is version 1.6 of the entry. See complete history

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

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

  • 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 ...

    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.


    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

    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Lysozyme CA129Gallus gallusMutation(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 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PT
Query on PT

Download Ideal Coordinates CCD File 
B [auth A], S [auth A], Y [auth A]PLATINUM (II) ION
Pt
HRGDZIGMBDGFTC-UHFFFAOYSA-N
 Ligand Interaction
BR
Query on BR

Download Ideal Coordinates CCD File 
C [auth A] , D [auth A] , E [auth A] , F [auth A] , G [auth A] , H [auth A] , I [auth A] , J [auth A] , 
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
 Ligand Interaction
DMS
Query on DMS

Download Ideal Coordinates CCD File 
U [auth A], V [auth A]DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

Download Ideal Coordinates CCD File 
W [auth A]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
X [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
T [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
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 = 78.58α = 90
b = 78.58β = 90
c = 37.29γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
xia2data reduction
MOSFLMdata reduction
Aimlessdata scaling
Cootmodel building
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


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

Revision History  (Full details and data files)

  • 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