6BEB

Crystal structure of VACV D13 in complex with Rifamycin SV


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.191 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Structural basis for the inhibition of poxvirus assembly by the antibiotic rifampicin.

Garriga, D.Headey, S.Accurso, C.Gunzburg, M.Scanlon, M.Coulibaly, F.

(2018) Proc. Natl. Acad. Sci. U.S.A. 115: 8424-8429


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Scaffold protein D13
A, B, C
576Vaccinia virus (strain Western Reserve)Mutation(s): 1 
Find proteins for P68440 (Vaccinia virus (strain Western Reserve))
Go to UniProtKB:  P68440
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FMT
Query on FMT

Download SDF File 
Download CCD File 
A, B, C
FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
 Ligand Interaction
RFV
Query on RFV

Download SDF File 
Download CCD File 
A
rifamycin SV
C37 H49 N O12
OUOULRWGQDSKTQ-ZVFQNIRDSA-N
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A, B, C
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.191 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 188.190α = 90.00
b = 188.190β = 90.00
c = 260.170γ = 120.00
Software Package:
Software NamePurpose
BUSTERrefinement
XSCALEdata scaling
Cootmodel building
XDSdata reduction
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Health and Medical Research Council (Australia)AustraliaAPP1051907

Revision History 

  • Version 1.0: 2018-07-18
    Type: Initial release
  • Version 1.1: 2018-08-01
    Type: Data collection, Database references
  • Version 1.2: 2018-08-15
    Type: Data collection, Database references
  • Version 1.3: 2018-08-22
    Type: Data collection, Database references
  • Version 1.4: 2019-02-20
    Type: Author supporting evidence, Data collection