5GNB

Crystal Structure of the Receptor Binding Domain of the Spike Glycoprotein of Human Betacoronavirus HKU1 (HKU1 1A-CTD, 2.3 angstrom, native-SAD phasing)

• PDB DOI: https://doi.org/10.2210/pdb5GNB/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Human coronavirus HKU1 (isolate N1)
• Expression System: Trichoplusia ni
• Mutation(s): No 


• Deposited: 2016-07-20 Released: 2017-06-07 
• Deposition Author(s): Guan, H., Wojdyla, J.A., Wang, M., Cui, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.219 
• R-Value Work: 0.173 
• R-Value Observed: 0.175 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 42.31 kDa 
• Atom Count: 3,201 
• Modelled Residue Count: 364 
• Deposited Residue Count: 371 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	A	371	Human coronavirus HKU1 (isolate N1)	Mutation(s): 0  Gene Names: S, 3
UniProt
Find proteins for Q5MQD0 (Human coronavirus HKU1 (isolate N1)) Explore Q5MQD0  Go to UniProtKB:  Q5MQD0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	B [auth A], C [auth A], D [auth A], E [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.219 
• R-Value Work: 0.173 
• R-Value Observed: 0.175 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.72	α = 90
b = 183.99	β = 90
c = 63.16	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
SHELXCD	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-06-07 
Deposition Author(s): Guan, H., Wojdyla, J.A., Wang, M., Cui, S.

Revision History  

• Version 1.0: 2017-06-07
  Type: Initial release
  
• Version 1.1: 2017-06-14
  Changes: Structure summary
• Version 1.2: 2017-09-27
  Changes: Data collection
• Version 1.3: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary