7LDJ

SARS-CoV-2 receptor binding domain in complex with WNb-2

• PDB DOI: https://doi.org/10.2210/pdb7LDJ/pdb

• Classification: VIRAL PROTEIN/IMMUNE SYSTEM
• Organism(s): Severe acute respiratory syndrome coronavirus 2, Vicugna pacos
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2021-01-13 Released: 2021-05-05 
• Deposition Author(s): Pymm, P., Dietrich, M.H., Tan, L.L., Adair, A., Tham, W.H.
• Funding Organization(s): National Health and Medical Research Council (NHMRC, Australia)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.36 Å
• R-Value Free: 0.268 
• R-Value Work: 0.210 
• R-Value Observed: 0.213 

Literature

SARS-CoV-2 receptor binding domain in complex with WNb-2

Pymm, P., Adair, A., Chan, L.J., Cooney, J.P., Mordant, F.L., Allison, C.C., Lopez, E., Haycroft, E., O'Neill, M.T., Tan, L.L., Dietrich, M.H., Drew, D., Doerflinger, M., Dengler, M., Scott, N.E., Wheatley, A.K., Gherardin, N.A., Venugopal, H., Cromer, D., Davenport, M.P., Pickering, R., Godfrey, D.I., Purcell, D.J., Kent, S.J., Chung, A.W., Subbarao, K., Pellegrini, M., Glukhova, A., Tham, W.H.

(2021) Proc Natl Acad Sci U S A 

• DOI: https://doi.org/10.1073/pnas.210191811

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Biological Assembly 4  

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

Biological assembly 4 assigned by authors.

Macromolecule Content

• Total Structure Weight: 149.12 kDa 
• Atom Count: 10,429 
• Modelled Residue Count: 1,287 
• Deposited Residue Count: 1,320 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	A [auth B], B [auth A], C, D	199	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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Nanobody 2	E, F, G, H	131	Vicugna pacos	Mutation(s): 0

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	I, K	4		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G86566TX GlyCosmos:  G86566TX GlyGen:  G86566TX

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	J	6		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G80946QO GlyCosmos:  G80946QO GlyGen:  G80946QO

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	M [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
PG4	N [auth E]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
MAN	L [auth A]	alpha-D-mannopyranose C6 H12 O6 WQZGKKKJIJFFOK-PQMKYFCFSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.36 Å
• R-Value Free: 0.268 
• R-Value Work: 0.210 
• R-Value Observed: 0.213 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.12	α = 90
b = 88.508	β = 90.4
c = 107.488	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-05-05 
Deposition Author(s): Pymm, P., Dietrich, M.H., Tan, L.L., Adair, A., Tham, W.H.

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Funding Organization	Location	Grant Number
National Health and Medical Research Council (NHMRC, Australia)	Australia	GNT2002073

Revision History  

• Version 1.0: 2021-05-05
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Database references, Refinement description