6LZG

Structure of novel coronavirus spike receptor-binding domain complexed with its receptor ACE2

• PDB DOI: https://doi.org/10.2210/pdb6LZG/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Homo sapiens, Severe acute respiratory syndrome coronavirus 2
• Expression System: Insect cell expression vector pTIE1
• Mutation(s): No 
• Membrane Protein: Yes  mpstruc


• Deposited: 2020-02-19 Released: 2020-03-18 
• Deposition Author(s): Wang, Q.H., Song, H., Qi, J.X.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.216 
• R-Value Work: 0.188 
• R-Value Observed: 0.190 

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: 93.5 kDa 
• Atom Count: 6,790 
• Modelled Residue Count: 791 
• Deposited Residue Count: 805 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Angiotensin-converting enzyme 2	A	596	Homo sapiens	Mutation(s): 0  Gene Names: ACE2, UNQ868/PRO1885 EC: 3.4.17.23 (PDB Primary Data), 3.4.17 (PDB Primary Data) Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BYF1 (Homo sapiens) Explore Q9BYF1  Go to UniProtKB:  Q9BYF1
PHAROS:  Q9BYF1 GTEx:  ENSG00000130234

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike protein S1	B	209	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0  Gene Names: S, 2 Membrane Entity: Yes
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], E [auth A], G [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
ZN (Subject of Investigation/LOI)	F [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.216 
• R-Value Work: 0.188 
• R-Value Observed: 0.190 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.448	α = 90
b = 104.448	β = 90
c = 229.786	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Blu-Ice	data collection
HKL-2000	data reduction
HKL-2000	data processing
PHASER	phasing
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-03-18 
Deposition Author(s): Wang, Q.H., Song, H., Qi, J.X.

Revision History  

• Version 1.0: 2020-03-18
  Type: Initial release
  
• Version 1.1: 2020-04-08
  Changes: Structure summary
• Version 2.0: 2020-04-22
  Type: Coordinate replacement
  Reason: Model orientation/position
  Changes: Advisory, Atomic model, Author supporting evidence, Database references, Polymer sequence, Refinement description, Source and taxonomy, Structure summary
• Version 2.1: 2020-05-06
  Changes: Database references, Source and taxonomy, Structure summary
• Version 2.2: 2020-05-27
  Changes: Database references
• Version 2.3: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 2.4: 2021-03-10
  Changes: Structure summary
• Version 2.5: 2023-11-29
  Changes: Data collection, Database references, Refinement description