7H6S

Group deposition for crystallographic fragment screening of Chikungunya virus nsP3 macrodomain -- Crystal structure of Chikungunya virus nsP3 macrodomain in complex with Z1162778919 (CHIKV_MacB-x0316)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.182 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

Group deposition for crystallographic fragment screening of Chikungunya virus nsP3 macrodomain

Aschenbrenner, J.C.Fairhead, M.Godoy, A.S.Balcomb, B.H.Capkin, E.Chandran, A.V.Dolci, I.Golding, M.Koekemoer, L.Lithgo, R.M.Marples, P.G.Ni, X.Oliva, G.Thompson, W.Tomlinson, C.W.E.Wild, C.Winokan, M.Xavier, M.-A.E.Fearon, D.von Delft, F.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Non-structural protein 3
A, B, C, D
163Chikungunya virusMutation(s): 0 
EC: 3.1.3.84
UniProt
Find proteins for Q8JUX6 (Chikungunya virus (strain S27-African prototype))
Explore Q8JUX6 
Go to UniProtKB:  Q8JUX6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8JUX6
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1AP3 (Subject of Investigation/LOI)
Query on A1AP3

Download Ideal Coordinates CCD File 
W [auth C]1-[(5-ethyl-1,2,4-oxadiazol-3-yl)methyl]pyridin-2(1H)-one
C10 H11 N3 O2
LLAHWSDSLKVDNQ-UHFFFAOYSA-N
TRS
Query on TRS

Download Ideal Coordinates CCD File 
H [auth A]2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
DMS
Query on DMS

Download Ideal Coordinates CCD File 
BA [auth D]
CA [auth D]
DA [auth D]
E [auth A]
EA [auth D]
BA [auth D],
CA [auth D],
DA [auth D],
E [auth A],
EA [auth D],
F [auth A],
G [auth A],
I [auth A],
J [auth A],
K [auth A],
O [auth A],
P [auth B],
Q [auth B],
T [auth B],
U [auth C],
X [auth C],
Y [auth C],
Z [auth C]
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
AA [auth C]
FA [auth D]
GA [auth D]
L [auth A]
M [auth A]
AA [auth C],
FA [auth D],
GA [auth D],
L [auth A],
M [auth A],
N [auth A],
R [auth B],
S [auth B],
V [auth C]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.182 
  • Space Group: P 31
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.12α = 90
b = 87.12β = 90
c = 85.566γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
REFMAC5refinement
Aimlessdata scaling
PHASERphasing
XDSdata reduction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesU19AI171292

Revision History  (Full details and data files)

  • Version 1.0: 2024-05-29
    Type: Initial release