5L3H

Re-refinement of 4dd4; cisplatin coordination chemistry determination at hen egg white lysozyme His15 with standard uncertainties

• PDB DOI: https://doi.org/10.2210/pdb5L3H/pdb
• Entry: 5L3H supersedes: 4DD4

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


• Deposited: 2016-05-06 Released: 2016-06-15 
• Deposition Author(s): Helliwell, J.R., Tanley, S.W.M.
• Funding Organization(s): Engineering and Physical Sciences Research Council

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.248 
• R-Value Work: 0.202 
• R-Value Observed: 0.204 

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 4dd4

Literature

Cisplatin coordination chemistry determination at hen egg white lysozyme His15 with ligand distances and angles, and their standard uncertainties, and also reporting a split occupancy effect

Helliwell, J.R., Schreurs, A.M.M., Kroon-Batenburg, L.M.J., Tanley, S.

(2016) ArXiv 

• DOI: https://doi.org/10.3927/45371856

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: 15.71 kDa 
• Atom Count: 1,147 
• 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	D [auth A], E [auth A], P [auth A], Q [auth A], R [auth A]	PLATINUM (II) ION Pt HRGDZIGMBDGFTC-UHFFFAOYSA-N
DMS	O [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
CL	B [auth A], F [auth A], G [auth A], K [auth A], L [auth A], M [auth A], N [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	C [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N
NH3	H [auth A], I [auth A], J [auth A]	AMMONIA H3 N QGZKDVFQNNGYKY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.248 
• R-Value Work: 0.202 
• R-Value Observed: 0.204 
• Space Group: P 4₃ 2₁ 2
• Diffraction Data: https://doi.org/10.15127/1.219233

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.832	α = 90
b = 78.832	β = 90
c = 37.021	γ = 90

Software Package:

Software Name	Purpose
PHASER	phasing
PHENIX	refinement

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2016-06-15 
Deposition Author(s): Helliwell, J.R., Tanley, S.W.M.
• This entry supersedes: 4DD4

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Funding Organization	Location	Grant Number
Engineering and Physical Sciences Research Council	United Kingdom	--

Revision History  

• Version 1.0: 2016-06-15
  Type: Initial release
  
• Version 1.1: 2016-09-28
  Changes: Database references
• Version 1.2: 2017-09-13
  Changes: Author supporting evidence
• Version 1.3: 2017-11-29
  Changes: Database references
• Version 1.4: 2018-08-08
  Changes: Data collection, Database references
• Version 1.5: 2024-01-10
  Changes: Data collection, Database references, Derived calculations, Refinement description