8QMC

High resolution structure of the Streptococcus pneumoniae topoisomerase IV-complex with the V-site 18mer dsDNA and novel fluoroquinolone Delafloxacin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.241 

Starting Model: experimental
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Ligand Structure Quality Assessment 


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Literature

The nature of the molecular interactions at high resolution of the Streptococcus pneumoniae topoisomerase IV-DNA complex with the novel fluoroquinolone Delafloxacin.

Najmudin, S.Pan, X.S.Wang, B.Chayen, N.E.Fisher, L.M.Sanderson, M.R.

To be published.

Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA topoisomerase (ATP-hydrolyzing),DNA topoisomerase 4 subunit A
A, B
742Streptococcus pneumoniaeMutation(s): 0 
Gene Names: AMCSP13_000989parCSP_0855
EC: 5.6.2.2
UniProt
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 GroupP72525
Sequence Annotations
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Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (5'-D(*T)-R(P*G)-D(P*T)-R(P*GP*GP*A)-D(P*T)-3')C [auth E]7DNA molecule
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Entity ID: 3
MoleculeChains LengthOrganismImage
DNA/RNA (5'-R(P*GP*G)-D(P*TP*T)-R(P*A)-D(P*T)-R(P*CP*CP*AP*CP*A)-3')D [auth F]11DNA molecule
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Entity ID: 4
MoleculeChains LengthOrganismImage
DNA/RNA (5'-R(P*AP*AP*CP*CP*G)-D(P*T)-R(P*A)-D(P*TP*T)-R(P*AP*C)-3')E [auth H]11DNA molecule
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Entity ID: 5
MoleculeChains LengthOrganismImage
DNA/RNA (5'-R(*G)-D(P*T)-R(P*AP*A)-D(P*T)-R(P*AP*C)-3')F [auth G]7DNA molecule
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
TE9 (Subject of Investigation/LOI)
Query on TE9

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T [auth F],
U [auth H]
delafloxacin
C18 H12 Cl F3 N4 O4
DYDCPNMLZGFQTM-UHFFFAOYSA-N
MPD
Query on MPD

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O [auth B](4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
MLA
Query on MLA

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G [auth A],
H [auth A]
MALONIC ACID
C3 H4 O4
OFOBLEOULBTSOW-UHFFFAOYSA-N
ACT
Query on ACT

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I [auth A],
J [auth A]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
CL
Query on CL

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N [auth A],
S [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG
Query on MG

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K [auth A]
L [auth A]
M [auth A]
P [auth B]
Q [auth B]
K [auth A],
L [auth A],
M [auth A],
P [auth B],
Q [auth B],
R [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.241 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 157.14α = 90
b = 157.14β = 90
c = 211.636γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
PDB-REDOrefinement
DIALSdata scaling
xia2data reduction
STARANISOdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Medical Research Council (MRC, United Kingdom)United KingdomMR/T000848/1

Revision History  (Full details and data files)

  • Version 1.0: 2024-10-02
    Type: Initial release