4KOE | pdb_00004koe

Quinolone(Trovafloxacin)-DNA cleavage complex of type IV topoisomerase from S. pneumoniae

PDB DOI: https://doi.org/10.2210/pdb4KOE/pdb
NAKB: 4KOE

Classification: ISOMERASE/DNA/INHIBITOR
Organism(s): Streptococcus pneumoniae TIGR4
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2013-05-11 Released: 2014-11-26
Deposition Author(s): Laponogov, I., Pan, X.-S., Veselkov, D.A., Fisher, L.M., Sanderson, M.R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.02 Å
R-Value Free:
0.210 (Depositor), 0.207 (DCC)
R-Value Work:
0.175 (Depositor), 0.172 (DCC)
R-Value Observed:
0.177 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Inhibitor-stabilised cleavage complexes of topoisomerase IIa: structural analysis of drug-dependent inter- and intramolecular interactions

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

To be published.

Macromolecule Content

Total Structure Weight: 185.66 kDa
Atom Count: 11,105
Modeled Residue Count: 1,415
Deposited Residue Count: 1,564
Unique protein chains: 2
Unique nucleic acid chains: 4

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA topoisomerase 4 subunit A	A, B	496	Streptococcus pneumoniae TIGR4	Mutation(s): 1 Gene Names: parC, SP_0855 EC: 5.99.1.3 (PDB Primary Data), 5.6.2.2 (UniProt)
UniProt
Find proteins for P72525 (Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4)) Explore P72525 Go to UniProtKB: P72525
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P72525
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA topoisomerase 4 subunit B	C, D	268	Streptococcus pneumoniae TIGR4	Mutation(s): 2 Gene Names: parE 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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q59961
Sequence Annotations Expand
Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 3
E-site DNA1	E	7	N/A
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Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 4
E-site DNA2	F	11	N/A
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Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 5
E-site DNA3	G	7	N/A
Sequence Annotations Expand
Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 6
E-site DNA4	H	11	N/A
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TR6 Query on TR6 Download:Ideal Coordinates CCD File SDF format, chain P [auth H] SDF format, chain O [auth F] MOL2 format, chain P [auth H] MOL2 format, chain O [auth F] mmCIF format, chain P [auth H] mmCIF format, chain O [auth F]	O [auth F], P [auth H]	Trovafloxacin C₂₀ H₁₅ F₃ N₄ O₃ WVPSKSLAZQPAKQ-CDMJZVDBSA-N		Interactions Focus chain O [auth F] Focus chain P [auth H] Interactions & Density Focus chain O [auth F] Focus chain P [auth H]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain N [auth D] SDF format, chain M [auth C] SDF format, chain L [auth B] SDF format, chain K [auth B] SDF format, chain J [auth A] SDF format, chain I [auth A] MOL2 format, chain N [auth D] MOL2 format, chain M [auth C] MOL2 format, chain L [auth B] MOL2 format, chain K [auth B] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] mmCIF format, chain N [auth D] mmCIF format, chain M [auth C] mmCIF format, chain L [auth B] mmCIF format, chain K [auth B] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A]	I [auth A] J [auth A] K [auth B] L [auth B] M [auth C] I [auth A], J [auth A], K [auth B], L [auth B], M [auth C], N [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth C] Focus chain N [auth D] Interactions & Density Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth C] Focus chain N [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.02 Å
R-Value Free: 0.210 (Depositor), 0.207 (DCC)
R-Value Work: 0.175 (Depositor), 0.172 (DCC)
R-Value Observed: 0.177 (Depositor)

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 158.04	α = 90
b = 158.04	β = 90
c = 210.42	γ = 120

Software Package:

Software Name	Purpose
GDE	data collection
PHASER	phasing
PHENIX	refinement
xia2	data reduction
XDS	data reduction
SCALA	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2014-11-26

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2014-11-26
Type: Initial release
Version 1.1: 2017-11-15
Changes: Refinement description
Version 1.2: 2024-11-06
Changes: Data collection, Database references, Derived calculations, Structure summary