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.

• PDB DOI: https://doi.org/10.2210/pdb5HQ1/pdb
• Entry: 5HQ1 supersedes: 4MWM

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


• Deposited: 2016-01-21 Released: 2016-05-18 
• Deposition Author(s): Helliwell, J.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.00 Å
• R-Value Free: 0.197 
• R-Value Work: 0.172 
• R-Value Observed: 0.173 

Starting Model: experimental

Re-refinement Note

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

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

• PubMed: 27226979 
• DOI: https://doi.org/10.1063/1.4948613
• Primary Citation of Related Structures:  
  5HMV, 5HQ1, 5I5Q, 5IDD

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Organizational Affiliation: 

School of Chemistry, University of Manchester , Manchester M13 9PL, United Kingdom.

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: 15.43 kDa 
• Atom Count: 1,108 
• Modelled Residue Count: 127 
• Deposited Residue Count: 128 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lysozyme C	A	128	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
PT	F [auth A], G [auth A], H [auth A], I [auth A]	PLATINUM (II) ION Pt HRGDZIGMBDGFTC-UHFFFAOYSA-N
DMS	B [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
NO3	D [auth A], E [auth A], K [auth A], L [auth A]	NITRATE ION N O3 NHNBFGGVMKEFGY-UHFFFAOYSA-N
CL	C [auth A], J [auth A], M [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.00 Å
• R-Value Free: 0.197 
• R-Value Work: 0.172 
• R-Value Observed: 0.173 
• Space Group: P 1
• Diffraction Data: https://doi.org/10.15127/1.266900

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 26.777	α = 88.9
b = 31.382	β = 72.31
c = 33.865	γ = 68.46

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• 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
  Changes: Database references
• Version 1.2: 2017-09-13
  Changes: Data collection
• Version 1.3: 2018-08-01
  Changes: Data collection, Database references
• Version 1.4: 2024-01-10
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.5: 2024-11-06
  Changes: Structure summary