5LXW

Atomic resolution X-ray crystal structure of cisplatin bound to hen egg white lysozyme stored for 5 years on the shelf

• PDB DOI: https://doi.org/10.2210/pdb5LXW/pdb

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


• Deposited: 2016-09-22 Released: 2016-10-05 
• Deposition Author(s): Helliwell, J.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.00 Å
• R-Value Free: 0.203 
• R-Value Work: 0.176 
• R-Value Observed: 0.177 

Literature

Atomic resolution X-ray crystal structure of cisplatin bound to hen egg white lysozyme stored for 5 years 'on the shelf'

Helliwell, J.R., Simon, T.

(2016) Zenodo 

• DOI: https://doi.org/10.5281/zenodo.155068

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: 15.23 kDa 
• Atom Count: 1,226 
• Modelled Residue Count: 129 
• Deposited Residue Count: 129 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lysozyme C	A	129	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 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PT	E [auth A], F [auth A], H [auth A]	PLATINUM (II) ION Pt HRGDZIGMBDGFTC-UHFFFAOYSA-N
DMS	B [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
CL	C [auth A], G [auth A], I [auth A], L [auth A], M [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	D [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N
NH3	J [auth A], K [auth A]	AMMONIA H3 N QGZKDVFQNNGYKY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.00 Å
• R-Value Free: 0.203 
• R-Value Work: 0.176 
• R-Value Observed: 0.177 
• Space Group: P 4₃ 2₁ 2
• Diffraction Data: https://doi.org/10.5281/zenodo.154704

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.37	α = 90
b = 79.37	β = 90
c = 37.84	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
iMOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-10-05 
Deposition Author(s): Helliwell, J.R.

Revision History  

• Version 1.0: 2016-10-05
  Type: Initial release
  
• Version 1.1: 2024-01-17
  Changes: Data collection, Database references, Derived calculations, Refinement description