5HQ1

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 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.172 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Re-refinement Note

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

  • 4MWM - 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
128Gallus gallusMutation(s): 0 
Gene 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 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PT
Query on PT

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

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Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
DMS
Query on DMS

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

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.172 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 26.777α = 88.90
b = 31.382β = 72.31
c = 33.865γ = 68.46
Software Package:
Software NamePurpose
SAINTdata reduction
APEXdata scaling
PHASERphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2016-01-21 
  • Released Date: 2016-05-18 
  • Deposition Author(s): Helliwell, J.R.
  • This entry supersedes: 4MWM

Revision History 

  • Version 1.0: 2016-05-18
    Type: Initial release
  • Version 1.1: 2016-07-27
    Type: Database references
  • Version 1.2: 2017-09-13
    Type: Data collection
  • Version 1.3: 2018-08-01
    Type: Data collection, Database references