6ZBP

H11-H4 complex with SARS-CoV-2

• PDB DOI: https://doi.org/10.2210/pdb6ZBP/pdb

• Classification: ANTIVIRAL PROTEIN
• Organism(s): Severe acute respiratory syndrome coronavirus 2, Lama glama
• Expression System: Homo sapiens, Escherichia coli
• Mutation(s): No 


• Deposited: 2020-06-08 Released: 2020-07-29 
• Deposition Author(s): Naismith, J.H., Huo, J., Mikolajek, H., Ward, P., Dumoux, M., Owens, R.J., LeBas, A.
• Funding Organization(s): Wellcome Trust

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.217 
• R-Value Work: 0.185 

Starting Model: experimental

Literature

H11-D4 complex with SARS-CoV-2 RBD

Naismith, J.H.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 39.08 kDa 
• Atom Count: 2,716 
• Modelled Residue Count: 323 
• Deposited Residue Count: 344 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	A [auth EEE]	210	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0  Gene Names: S, 2
UniProt
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTC2  Go to UniProtKB:  P0DTC2
Glycosylation
Glycosylation Sites: 1		Go to GlyGen: P0DTC2-1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
H11-H4	B [auth FFF]	134	Lama glama	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	C [auth EEE]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
SO4	D [auth FFF]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.217 
• R-Value Work: 0.185 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.15	α = 90
b = 73.15	β = 90
c = 131.67	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XSCALE	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-07-29 
Deposition Author(s): Naismith, J.H., Huo, J., Mikolajek, H., Ward, P., Dumoux, M., Owens, R.J., LeBas, A.

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Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	100209/Z/12/Z

Revision History  

• Version 1.0: 2020-07-29
  Type: Initial release
  
• Version 1.1: 2024-01-24
  Changes: Data collection, Database references, Derived calculations, Refinement description