7OAQ

Nanobody H3 AND C1 bound to RBD with Kent mutation

• PDB DOI: https://doi.org/10.2210/pdb7OAQ/pdb

• Classification: ANTIVIRAL PROTEIN
• Organism(s): Lama glama, Severe acute respiratory syndrome coronavirus 2
• Expression System: Escherichia coli, Homo sapiens
• Mutation(s): Yes 


• Deposited: 2021-04-20 Released: 2021-08-11 
• Deposition Author(s): Naismith, J.H., Mikolajek, H.
• Funding Organization(s): Wellcome Trust, Engineering and Physical Sciences Research Council

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 0.178 
• R-Value Work: 0.155 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 54.01 kDa 
• Atom Count: 3,991 
• Modelled Residue Count: 448 
• Deposited Residue Count: 477 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
H3	A [auth AAA]	131	Lama glama	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike protein S1	B [auth EEE]	210	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 1  Gene Names: S, 2
UniProt
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTC2  Go to UniProtKB:  P0DTC2

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
H3	C [auth FFF]	136	Lama glama	Mutation(s): 0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	D [auth EEE]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
CIT	E [auth EEE]	CITRIC ACID C6 H8 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-N
CL	F [auth FFF]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 0.178 
• R-Value Work: 0.155 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.857	α = 90
b = 105.857	β = 90
c = 112.709	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
xia2	data reduction
xia2	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-08-11 
Deposition Author(s): Naismith, J.H., Mikolajek, H.

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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: 2021-08-11
  Type: Initial release
  
• Version 2.0: 2021-10-06
  Changes: Atomic model, Data collection, Database references
• Version 2.1: 2024-01-31
  Changes: Data collection, Derived calculations, Refinement description