6YZ5 | pdb_00006yz5

H11-D4 complex with SARS-CoV-2 RBD

• PDB DOI: https://doi.org/10.2210/pdb6YZ5/pdb

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


• Deposited: 2020-05-06 Released: 2020-06-03 
• Deposition Author(s): Naismith, J.H., Huo, J., Mikolajek, H., Ward, P., Dumoux, M., Owens, R.J., Le Bas, A.
• Funding Organization(s): Wellcome Trust, Engineering and Physical Sciences Research Council

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.193 (Depositor), 0.203 (DCC) 
• R-Value Work: 
  0.166 (Depositor) 
• R-Value Observed: 
  0.167 (Depositor) 

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 and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 39.93 kDa 
• Atom Count: 2,919 
• Modeled Residue Count: 322 
• Deposited Residue Count: 344 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	A [auth E]	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
Nanobody H11-D4	B [auth F]	134	Lama glama	Mutation(s): 0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	C [auth E]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
EDO	D [auth E], E, F [auth E], G [auth E], H [auth E], I [auth E], J [auth E], M [auth E], N [auth E], O [auth E], P [auth E], Q [auth F]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACT	K [auth E], L [auth E], R [auth F], S [auth F]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.193 (Depositor), 0.203 (DCC) 
• R-Value Work:  0.166 (Depositor) 
• R-Value Observed: 0.167 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.28	α = 90
b = 78.28	β = 90
c = 127.09	γ = 120

Software Package:

Software Name	Purpose
XDS	data reduction
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-06-03 
Deposition Author(s): Naismith, J.H., Huo, J., Mikolajek, H., Ward, P., Dumoux, M., Owens, R.J., Le Bas, A.

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Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	100209/Z/12/Z
Engineering and Physical Sciences Research Council	United Kingdom	EP/S025243/1.

Revision History  

• Version 1.0: 2020-06-03
  Type: Initial release
  
• Version 1.1: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.2: 2024-01-24
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 1.3: 2024-11-13
  Changes: Structure summary