9FWK | pdb_00009fwk

Ensemble model of ligand-free SARS-CoV-2 NSP10-NSP14 (ExoN) and in complex with partially bound VT00123


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.51 Å
  • R-Value Free: 
    0.199 (Depositor), 0.194 (DCC) 
  • R-Value Work: 
    0.183 (Depositor), 0.178 (DCC) 
  • R-Value Observed: 
    0.184 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

Ensemble model of ligand-free SARS-CoV-2 NSP10-NSP14 (ExoN) and in complex with partially bound VT00123

Krojer, T.Kozielski, F.Sele, C.Nyblom, M.Fisher, S.Z.Knecht, W.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Non-structural protein 10131Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
UniProt
Find proteins for P0DTC1 (Severe acute respiratory syndrome coronavirus 2)
Explore P0DTC1 
Go to UniProtKB:  P0DTC1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DTC1
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine-N7 methyltransferase nsp14290Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
Gene Names: rep1a-1b
EC: 2.1.1.56 (PDB Primary Data), 3.1.13 (PDB Primary Data)
UniProt
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2)
Explore P0DTD1 
Go to UniProtKB:  P0DTD1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DTD1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1IGS (Subject of Investigation/LOI)
Query on A1IGS

Download Ideal Coordinates CCD File 
I [auth B](4R)-4-pyridin-4-ylpyrrolidin-2-one
C9 H10 N2 O
NGECHVBQXAJIFW-UHFFFAOYSA-N
A1IGT (Subject of Investigation/LOI)
Query on A1IGT

Download Ideal Coordinates CCD File 
E [auth A](4S)-4-pyridin-4-ylpyrrolidin-2-one
C9 H10 N2 O
NGECHVBQXAJIFW-MRVPVSSYSA-N
DMS
Query on DMS

Download Ideal Coordinates CCD File 
F [auth B]DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
G [auth B],
H [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.51 Å
  • R-Value Free:  0.199 (Depositor), 0.194 (DCC) 
  • R-Value Work:  0.183 (Depositor), 0.178 (DCC) 
  • R-Value Observed: 0.184 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.059α = 90
b = 99.711β = 114.73
c = 51.182γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
autoPROCdata processing
XDSdata reduction
Aimlessdata scaling
TRUNCATEdata processing
DIMPLEphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-08-20
    Type: Initial release