7CDI

Crystal structure of SARS-CoV-2 antibody P2C-1F11 with RBD

• PDB DOI: https://doi.org/10.2210/pdb7CDI/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Severe acute respiratory syndrome coronavirus 2, Homo sapiens
• Expression System: Spodoptera frugiperda, Homo sapiens
• Mutation(s): No 


• Deposited: 2020-06-19 Released: 2020-11-18 
• Deposition Author(s): Wang, X., Zhang, L., Ge, J., Wang, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.96 Å
• R-Value Free: 0.254 
• R-Value Work: 0.202 
• R-Value Observed: 0.205 

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.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 70.95 kDa 
• Atom Count: 4,715 
• Modelled Residue Count: 615 
• Deposited Residue Count: 648 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike protein S1	A [auth E]	217	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
antibody P2C-1F11 heavy chain	B [auth H]	217	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
antibody P2C-1F11 light chain	C [auth L]	214	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	D [auth E]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.96 Å
• R-Value Free: 0.254 
• R-Value Work: 0.202 
• R-Value Observed: 0.205 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 194.88	α = 90
b = 85.39	β = 100.29
c = 58.51	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-11-18 
Deposition Author(s): Wang, X., Zhang, L., Ge, J., Wang, R.

Revision History  

• Version 1.0: 2020-11-18
  Type: Initial release
  
• Version 1.1: 2021-12-01
  Changes: Database references
• Version 1.2: 2023-11-29
  Changes: Data collection, Refinement description