5L3I

Re-refinement of 4dd6; cisplatin coordination chemistry determination at hen egg white lysozyme His15

  • Classification: HYDROLASE
  • Organism(s): Gallus gallus

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.181 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

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 --: --


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Lysozyme C
A
129Gallus 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 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

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

Download SDF File 
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
NH3
Query on NH3

Download SDF File 
Download CCD File 
A
AMMONIA
H3 N
QGZKDVFQNNGYKY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.181 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 78.016α = 90.00
b = 78.016β = 90.00
c = 37.071γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2016-05-06 
  • Released Date: 2016-06-15 
  • Deposition Author(s): Helliwell, J.R.
  • This entry supersedes: 4DD6

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

Revision History 

  • Version 1.0: 2016-06-15
    Type: Initial release
  • Version 1.1: 2016-09-28
    Type: Database references
  • Version 1.2: 2017-09-13
    Type: Author supporting evidence