4Z4Q

Quinazolinedione(PD 0305970)-DNA cleavage complex of topoisomerase IV from S. pneumoniae


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.04 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.164 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Structural studies of the drug-stabilized cleavage complexes of topoisomerase IV and gyrase from Streptococcus pneumoniae

Laponogov, I.Veselkov, D.A.Pan, X.-S.Selvarajah, J.Crevel, I.M.-T.Fisher, L.M.Sanderson, M.R.

To be published.

Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA topoisomerase 4 subunit B,DNA topoisomerase 4 subunit AA, B742Streptococcus pneumoniae TIGR4Mutation(s): 0 
Gene Names: parESP_0852parCSP_0855
EC: 5.99.1.3 (PDB Primary Data), 5.6.2.2 (UniProt)
UniProt
Find proteins for Q59961 (Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4))
Explore Q59961 
Go to UniProtKB:  Q59961
Find proteins for P72525 (Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4))
Explore P72525 
Go to UniProtKB:  P72525
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsQ59961P72525
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsLengthOrganismImage
V-site DNAC [auth E]7pBR322 based IG-lambda expression vector
Protein Feature View
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  • Reference Sequence

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Entity ID: 3
MoleculeChainsLengthOrganismImage
V-site DNAD [auth F]11pBR322 based IG-lambda expression vector
Protein Feature View
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  • Reference Sequence

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Entity ID: 4
MoleculeChainsLengthOrganismImage
V-site DNAE [auth G]7pBR322 based IG-lambda expression vector
Protein Feature View
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  • Reference Sequence

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Entity ID: 5
MoleculeChainsLengthOrganismImage
V-site DNAF [auth H]11pBR322 based IG-lambda expression vector
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PDQ
Query on PDQ

Download Ideal Coordinates CCD File 
K [auth F],
L [auth H]
3-amino-7-{(3R)-3-[(1S)-1-aminoethyl]pyrrolidin-1-yl}-1-cyclopropyl-6-fluoro-8-methylquinazoline-2,4(1H,3H)-dione
C18 H24 F N5 O2
SMONLCFJGCJROJ-WDEREUQCSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
G [auth A],
H [auth A],
I [auth B],
J [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.04 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.164 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 158.02α = 90
b = 158.02β = 90
c = 211.22γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
xia2data reduction
xia2data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research CouncilUnited KingdomBB/K010069/1

Revision History  (Full details and data files)

  • Version 1.0: 2016-09-14
    Type: Initial release
  • Version 1.1: 2017-08-30
    Changes: Author supporting evidence, Derived calculations