5IDD

Comment on S. W. M. Tanley and J. R. Helliwell Structural dynamics of cisplatin binding to histidine in a protein Struct. Dyn. 1, 034701 (2014) regarding the refinement of 4mwk, 4mwm, 4mwn and 4oxe and the method we have adopted.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.13 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.177 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Re-refinement Note

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

  • 4OXE - determined by Tanley, S.W.M., Helliwell, J.R.  

Literature

Comment on "Structural dynamics of cisplatin binding to histidine in a protein" [Struct. Dyn. 1, 034701 (2014)].

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

(2016) Struct Dyn. 3: 037101-037101


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Lysozyme C
A
129Gallus gallusGene 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 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
PT
Query on PT

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Download CCD File 
A
PLATINUM (II) ION
Pt
HRGDZIGMBDGFTC-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

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Download CCD File 
A
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
DMS
Query on DMS

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Download CCD File 
A
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
NO3
Query on NO3

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Download CCD File 
A
NITRATE ION
N O3
NHNBFGGVMKEFGY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.13 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.177 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 26.957α = 88.76
b = 31.794β = 71.99
c = 34.055γ = 68.33
Software Package:
Software NamePurpose
APEX 2data scaling
PHASERphasing
REFMACrefinement
SAINTdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationCountryGrant Number
Engineering and Physical Sciences Research CouncilUnited Kingdom--

Revision History 

  • Version 1.0: 2016-05-18
    Type: Initial release
  • Version 1.1: 2016-07-20
    Type: Database references
  • Version 1.2: 2017-09-13
    Type: Author supporting evidence, Data collection