7UXZ

Crystal structure of SARS-CoV-2 nucleocapsid protein C-terminal domain complexed with Chicoric acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.73 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.174 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

Discovery and structural characterization of chicoric acid as a SARS-CoV-2 nucleocapsid protein ligand and RNA binding disruptor

Bezerra, E.H.S.Mercaldi, G.F.Batista, F.A.H.Tonoli, C.C.C.Shimizu, J.F.Soprano, A.S.da Silva, J.C.Ribeiro Filho, H.V.Faria, J.N.Cunha, M.G.Nagai, A.Bajgelman, M.C.Rocco, S.A.Bruder, M.C.P.Oliveira, P.S.L.Cordeiro, A.T.Marques, R.E.Franchini, K.G.Sforca, M.L.Benedetti, C.E.Figueira, A.C.M.Trivella, D.B.B.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Nucleoprotein114Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
Gene Names: N
UniProt
Find proteins for P0DTC9 (Severe acute respiratory syndrome coronavirus 2)
Explore P0DTC9 
Go to UniProtKB:  P0DTC9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DTC9
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GKP (Subject of Investigation/LOI)
Query on GKP

Download Ideal Coordinates CCD File 
G [auth AAA](2R,3R)-2,3-bis{[(2E)-3-(3,4-dihydroxyphenyl)prop-2-enoyl]oxy}butanedioic acid
C22 H18 O12
YDDGKXBLOXEEMN-IABMMNSOSA-N
 Ligand Interaction
PEG
Query on PEG

Download Ideal Coordinates CCD File 
H [auth AAA],
M [auth FFF]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
I [auth AAA],
K [auth DDD],
N [auth FFF]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
L [auth EEE]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
J [auth AAA]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.73 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.174 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.669α = 90
b = 120.655β = 90
c = 128.503γ = 90
Software Package:
Software NamePurpose
MxCuBEdata collection
autoPROCdata reduction
PHASERphasing
REFMACrefinement
autoPROCdata processing

Structure Validation

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Ligand Structure Quality Assessment 



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other governmentBrazil01.20.0003.00
Other governmentBrazil--
Other governmentBrazil--

Revision History  (Full details and data files)

  • Version 1.0: 2022-06-22
    Type: Initial release