5LVK | pdb_00005lvk

Human Lysozyme co-crystallized with [H2Ind][trans-RuCl4(DMSO)(HInd)]

PDB DOI: https://doi.org/10.2210/pdb5LVK/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2016-09-14 Released: 2016-09-28
Deposition Author(s): Kurpiewska, K., Szura, A., Lewinski, K.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.49 Å
R-Value Free:
0.281 (Depositor), 0.281 (DCC)
R-Value Work:
0.177 (Depositor), 0.177 (DCC)
R-Value Observed:
0.188 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Ligand-dependent interaction of anticancer ruthenium complexes with hen egg white lysozyme and human lysozyme

Oszajca, M., Kurpiewska, K., Halajko, P., Szura, A., Lewinski, K., Brindell, M.

To be published.

Macromolecule Content

Total Structure Weight: 30.24 kDa
Atom Count: 2,354
Modeled Residue Count: 260
Deposited Residue Count: 260
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lysozyme C	A, B	130	Homo sapiens	Mutation(s): 0 Gene Names: LYZ, LZM EC: 3.2.1.17
UniProt & NIH Common Fund Data Resources
Find proteins for P61626 (Homo sapiens) Explore P61626 Go to UniProtKB: P61626
PHAROS: P61626 GTEx: ENSG00000090382
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P61626
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
RU Query on RU Download:Ideal Coordinates CCD File SDF format, chain M [auth B] SDF format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain L [auth B]	L [auth B], M [auth B]	RUTHENIUM ION Ru BPEVHDGLPIIAGH-UHFFFAOYSA-N		Interactions Focus chain L [auth B] Focus chain M [auth B] Interactions & Density Focus chain L [auth B] Focus chain M [auth B]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A], E [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A]
NO3 Query on NO3 Download:Ideal Coordinates CCD File SDF format, chain P [auth B] MOL2 format, chain P [auth B] mmCIF format, chain P [auth B]	P [auth B]	NITRATE ION N O₃ NHNBFGGVMKEFGY-UHFFFAOYSA-N		Interactions Focus chain P [auth B] Interactions & Density Focus chain P [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain N [auth B] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] MOL2 format, chain N [auth B] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] mmCIF format, chain N [auth B] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A]	F [auth A], G [auth A], H [auth A], I [auth A], N [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain N [auth B] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain N [auth B]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain O [auth B] SDF format, chain K [auth A] SDF format, chain J [auth A] MOL2 format, chain O [auth B] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] mmCIF format, chain O [auth B] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A]	J [auth A], K [auth A], O [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain K [auth A] Focus chain O [auth B] Interactions & Density Focus chain J [auth A] Focus chain K [auth A] Focus chain O [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.49 Å
R-Value Free: 0.281 (Depositor), 0.281 (DCC)
R-Value Work: 0.177 (Depositor), 0.177 (DCC)
R-Value Observed: 0.188 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.039	α = 90
b = 64.1	β = 90
c = 111.311	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
CrysalisPro	data reduction
PHASER	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2016-09-28

Deposition Author(s):

Kurpiewska, K.

Szura, A.

Lewinski, K.

Revision History (Full details and data files)

Version 1.0: 2016-09-28
Type: Initial release
Version 1.1: 2023-12-20
Changes: Data collection, Database references, Derived calculations, Structure summary
Version 1.2: 2024-01-17
Changes: Refinement description
Version 1.3: 2024-11-13
Changes: Structure summary