5LSH

human lysozyme in complex with a tetrasaccharide fragment of the O-chain of LPS from Klebsiella pneumoniae

• PDB DOI: https://doi.org/10.2210/pdb5LSH/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Mus musculus
• Mutation(s): No 


• Deposited: 2016-08-26 Released: 2017-06-21 
• Deposition Author(s): Zhang, R., Nifantiev, N.E., Krylov, V., Luetteke, T., Scheidig, A.J., Siebert, H.-C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.06 Å
• R-Value Free: 0.203 
• R-Value Work: 0.180 
• R-Value Observed: 0.181 

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: 15.56 kDa 
• Atom Count: 1,414 
• Modelled Residue Count: 130 
• Deposited Residue Count: 130 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lysozyme C	A	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

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-galactopyranose-(1-3)-beta-D-galactofuranose-(1-3)-alpha-D-galactopyranose-(1-3)-propyl beta-D-galactofuranoside	B	4	N/A	N/A
Glycosylation Resources
GlyTouCan:  G41009JY GlyCosmos:  G41009JY

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	C [auth A], D [auth A], E [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	F [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.06 Å
• R-Value Free: 0.203 
• R-Value Work: 0.180 
• R-Value Observed: 0.181 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 33.108	α = 90
b = 56.04	β = 90
c = 60.531	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-06-21 
Deposition Author(s): Zhang, R., Nifantiev, N.E., Krylov, V., Luetteke, T., Scheidig, A.J., Siebert, H.-C.

Revision History  

• Version 1.0: 2017-06-21
  Type: Initial release
  
• Version 1.1: 2017-12-27
  Changes: Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
• Version 2.1: 2024-01-17
  Changes: Data collection, Database references, Refinement description, Structure summary