7C8V

Structure of sybody SR4 in complex with the SARS-CoV-2 S Receptor Binding domain (RBD)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.186 

wwPDB Validation 3D Report Full Report



Literature

Potent synthetic nanobodies against SARS-CoV-2 and molecular basis for neutratlization

Li, T.Cai, H.Yao, H.Zhou, B.Zhao, Y.Qin, W.Lavillette, D.Li, D.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Synthetic nanobody SR4
A
144synthetic constructMutation(s): 0 
Protein Feature View
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Spike glycoprotein
B
213Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
Gene Names: S2
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2)
Go to UniProtKB:  P0DTC2
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download CCD File 
B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
GOL
Query on GOL

Download CCD File 
A, B
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.186 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.553α = 90
b = 65.553β = 90
c = 344.526γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Chinese Academy of SciencesChinaQYZDB-SSW-SMC037, XDB37020204
National Science Foundation (NSF, China)China31870726

Revision History 

  • Version 1.0: 2020-06-24
    Type: Initial release