5LXW | pdb_00005lxw

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.00 Å
R-Value Free:
0.203 (Depositor), 0.209 (DCC)
R-Value Work:
0.176 (Depositor)
R-Value Observed:
0.177 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

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

Macromolecule Content

Total Structure Weight: 15.23 kDa
Atom Count: 1,226
Modeled Residue Count: 129
Deposited Residue Count: 129
Unique protein chains: 1

Macromolecules

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| 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00698
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PT Query on PT Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain H [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain H [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain H [auth A]	E [auth A], F [auth A], H [auth A]	PLATINUM (II) ION Pt HRGDZIGMBDGFTC-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth A] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth A]
DMS Query on DMS Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain G [auth A] SDF format, chain I [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] MOL2 format, chain C [auth A] MOL2 format, chain G [auth A] MOL2 format, chain I [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] mmCIF format, chain C [auth A] mmCIF format, chain G [auth A] mmCIF format, chain I [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A]	C [auth A], G [auth A], I [auth A], L [auth A], M [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Focus chain G [auth A] Focus chain I [auth A] Focus chain L [auth A] Focus chain M [auth A] Interactions & Density Focus chain C [auth A] Focus chain G [auth A] Focus chain I [auth A] Focus chain L [auth A] Focus chain M [auth A]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
NH3 Query on NH3 Download:Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A]	J [auth A], K [auth A]	AMMONIA H₃ N QGZKDVFQNNGYKY-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain K [auth A] Interactions & Density Focus chain J [auth A] Focus chain K [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.00 Å
R-Value Free: 0.203 (Depositor), 0.209 (DCC)
R-Value Work: 0.176 (Depositor)
R-Value Observed: 0.177 (Depositor)

Diffraction Data:

Space Group: P 4₃ 2₁ 2

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

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Entry History

Deposition Data

Released Date: 2016-10-05

Deposition Author(s):

Helliwell, J.R.

Revision History (Full details and data files)

Version 1.0: 2016-10-05
Type: Initial release
Version 1.1: 2024-01-17
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.2: 2024-11-06
Changes: Structure summary