7DHX | pdb_00007dhx

Crystal structure of SARS-CoV-2 RBD binding to pangolin ACE2

• PDB DOI: https://doi.org/10.2210/pdb7DHX/pdb

• Classification: STRUCTURAL PROTEIN
• Organism(s): Manis javanica, Severe acute respiratory syndrome coronavirus 2
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2020-11-17 Released: 2021-09-29 
• Deposition Author(s): Wang, Q.H., Qi, J.X., Wu, L.L.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.235 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.194 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.196 (Depositor) 

Starting Model: experimental

Literature

Molecular basis of pangolin ACE2 engaged by COVID-19 virus

Wu, L., Gao, G., Yan, J., Wang, Q., Niu, S., Chen, Q., Qi, J., Zhang, Y., Jiaqi, S., Shi, Y.

(2021) Chin Sci Bull 66: 73-84

• DOI: https://doi.org/10.1360/TB-2020-1372

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 93.97 kDa 
• Atom Count: 6,641 
• Modeled Residue Count: 788 
• Deposited Residue Count: 810 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
pangolin ACE2	A	601	Manis javanica	Mutation(s): 0  EC: 3.4
UniProt
Find proteins for A0A8M0FGR3 (Manis javanica) Explore A0A8M0FGR3  Go to UniProtKB:  A0A8M0FGR3
Glycosylation
Glycosylation Sites: 2

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	B	209	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

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.235 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.194 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.196 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 139.996	α = 90
b = 97.564	β = 129.154
c = 90.982	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-09-29 
Deposition Author(s): Wang, Q.H., Qi, J.X., Wu, L.L.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	81922044

Revision History  

• Version 1.0: 2021-09-29
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description
• Version 1.2: 2024-11-13
  Changes: Structure summary