8C3E | pdb_00008c3e

Engineered mini-protein LCB2 (blocking ligand of SARS-Cov-2 spike protein)

• PDB DOI: https://doi.org/10.2210/pdb8C3E/pdb

• Classification: ANTIVIRAL PROTEIN
• Organism(s): synthetic construct
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2022-12-23 Released: 2023-04-12 
• Deposition Author(s): Korban, S.A., Mikhailovskii, O.V., Luzik, D.A., Gurzhiy, V.V., Levkina, A.D., Kharkov, B.B., Skrynnikov, N.R.
• Funding Organization(s): St. Petersburg State University

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.249 (Depositor), 0.247 (DCC) 
• R-Value Work: 
  0.209 (Depositor), 0.209 (DCC) 
• R-Value Observed: 
  0.220 (Depositor) 

Starting Model: in silico

Literature

Engineered mini-protein LCB2 (blocking ligand of SARS-Cov-2 spike protein)

Korban, S.A., Mikhailovskii, O.V., Luzik, D.A., Gurzhiy, V.V., Levkina, A.D., Kharkov, B.B., Skrynnikov, N.R.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly Evidence: NMR relaxation study

Macromolecule Content

• Total Structure Weight: 7.3 kDa 
• Atom Count: 511 
• Modelled Residue Count: 55 
• Deposited Residue Count: 58 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Engineered protein LCB2	A	58	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	B [auth A], C [auth A], D [auth A], E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.249 (Depositor), 0.247 (DCC) 
• R-Value Work:  0.209 (Depositor), 0.209 (DCC) 
• R-Value Observed: 0.220 (Depositor) 

Diffraction Data: https://doi.org/10.5281/zenodo.14555180

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.817	α = 90
b = 57.817	β = 90
c = 41.54	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
CrysalisPro	data collection
autoPROC	data processing
autoPROC	data reduction
autoPROC	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-04-12 
Deposition Author(s): Korban, S.A., Mikhailovskii, O.V., Luzik, D.A., Gurzhiy, V.V., Levkina, A.D., Kharkov, B.B., Skrynnikov, N.R.

---

Funding Organization	Location	Grant Number
St. Petersburg State University	Russian Federation	94031251

Revision History  

• Version 1.0: 2023-04-12
  Type: Initial release
  
• Version 1.1: 2024-06-19
  Changes: Data collection
• Version 2.0: 2025-01-22
  Type: Coordinate replacement
  Reason: Model completeness
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Refinement description, Structure summary