2DD8

Crystal Structure of SARS-CoV Spike Receptor-Binding Domain Complexed with Neutralizing Antibody

• PDB DOI: https://doi.org/10.2210/pdb2DD8/pdb

• Classification: IMMUNE SYSTEM/VIRAL PROTEIN
• Organism(s): Homo sapiens, Severe acute respiratory syndrome-related coronavirus
• Expression System: Escherichia coli, Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2006-01-24 Released: 2006-04-04 
• Deposition Author(s): Prabakaran, P., Gan, J.H., Feng, Y., Zhu, Z.Y., Xiao, X.D., Ji, X., Dimitrov, D.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.261 
• R-Value Work: 0.199 
• R-Value Observed: 0.199 

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 71.86 kDa 
• Atom Count: 5,057 
• Modelled Residue Count: 624 
• Deposited Residue Count: 660 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
IGG Heavy Chain	A [auth H]	245	Homo sapiens	Mutation(s): 0  Gene Names: recombinant antibody Fab

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
IGG Light Chain	B [auth L]	213	Homo sapiens	Mutation(s): 0  Gene Names: recombinant antibody Fab
UniProt
Find proteins for Q8N355 (Homo sapiens) Explore Q8N355  Go to UniProtKB:  Q8N355

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	C [auth S]	202	Severe acute respiratory syndrome-related coronavirus	Mutation(s): 0  Gene Names: Tor2
UniProt
Find proteins for P59594 (Severe acute respiratory syndrome coronavirus) Explore P59594  Go to UniProtKB:  P59594

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	E [auth S]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
PO4	D [auth H]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.261 
• R-Value Work: 0.199 
• R-Value Observed: 0.199 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.693	α = 90
b = 68.611	β = 98.08
c = 80.085	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-04-04 
Deposition Author(s): Prabakaran, P., Gan, J.H., Feng, Y., Zhu, Z.Y., Xiao, X.D., Ji, X., Dimitrov, D.S.

Revision History  

• Version 1.0: 2006-04-04
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.4: 2023-08-30
  Changes: Data collection, Database references, Structure summary
• Version 1.5: 2023-10-25
  Changes: Refinement description