7W6U | pdb_00007w6u

Structure of SARS-CoV-2 spike receptor-binding domain complexed with its receptor equine ACE2

• PDB DOI: https://doi.org/10.2210/pdb7W6U/pdb

• Classification: VIRAL PROTEIN/INHIBITOR
• Organism(s): Equus caballus, Severe acute respiratory syndrome coronavirus 2
• Expression System: Escherichia coli, Homo sapiens
• Mutation(s): No 


• Deposited: 2021-12-02 Released: 2022-06-08 
• Deposition Author(s): Xu, Z.P., Liu, K.F., Han, P., Qi, J.X.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.56 Å
• R-Value Free: 
  0.227 (Depositor), 0.224 (DCC) 
• R-Value Work: 
  0.193 (Depositor), 0.192 (DCC) 
• R-Value Observed: 
  0.195 (Depositor) 

Starting Model: experimental

Literature

Binding and structural basis of equine ACE2 to RBDs from SARS-CoV, SARS-CoV-2 and related coronaviruses

Xu, Z., Kang, X., Han, P., Du, P., Li, L., Zheng, A., Deng, C., Qi, J., Zhao, X., Wang, Q., Liu, K., Gao, G.F.

(2022) Nat Commun 13: 3547

• DOI: https://doi.org/10.1038/s41467-022-31276-6

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 96.02 kDa 
• Atom Count: 6,440 
• Modeled Residue Count: 785 
• Deposited Residue Count: 831 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Angiotensin-converting enzyme	A	602	Equus caballus	Mutation(s): 0  Gene Names: ACE2 EC: 3.4.17.23 (PDB Primary Data), 3.4 (UniProt)
UniProt
Find proteins for F6V9L3 (Equus caballus) Explore F6V9L3  Go to UniProtKB:  F6V9L3

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike protein S1	B	229	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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG (Subject of Investigation/LOI)	D [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
ZN (Subject of Investigation/LOI)	C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.56 Å
• R-Value Free:  0.227 (Depositor), 0.224 (DCC) 
• R-Value Work:  0.193 (Depositor), 0.192 (DCC) 
• R-Value Observed: 0.195 (Depositor) 

Space Group: I 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 195.57	α = 90
b = 195.57	β = 90
c = 149.77	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-06-08 
Deposition Author(s): Xu, Z.P., Liu, K.F., Han, P., Qi, J.X.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	32100752

Revision History  

• Version 1.0: 2022-06-08
  Type: Initial release
  
• Version 1.1: 2022-10-12
  Changes: Source and taxonomy, Structure summary
• Version 1.2: 2022-12-21
  Changes: Database references
• Version 1.3: 2023-11-29
  Changes: Data collection, Refinement description
• Version 1.4: 2024-10-16
  Changes: Structure summary