4K4O

The DNA Gyrase B ATP binding domain of Enterococcus faecalis in complex with a small molecule inhibitor

PDB DOI: https://doi.org/10.2210/pdb4K4O/pdb

Classification: ISOMERASE/ISOMERASE INHIBITOR
Organism(s): Enterococcus faecalis V583
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2013-04-12 Released: 2014-01-15
Deposition Author(s): Bensen, D.C., Akers-Rodriguez, S., Lam, T., Tari, L.W.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.30 Å
R-Value Free: 0.196
R-Value Work: 0.178
R-Value Observed: 0.179

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

A new class of type IIA topoisomerase inhibitors with broad-spectrum antibacterial activity

Tari, L.W., Bensen, D.C., Finn, J.

To be published.

Macromolecule Content

Total Structure Weight: 24.34 kDa
Atom Count: 1,802
Modelled Residue Count: 190
Deposited Residue Count: 215
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA gyrase subunit B	A	215	Enterococcus faecalis V583	Mutation(s): 0 Gene Names: EF_0005, gyrB EC: 5.99.1.3 (PDB Primary Data), 5.6.2.2 (UniProt)
UniProt
Find proteins for Q839Z1 (Enterococcus faecalis (strain ATCC 700802 / V583)) Explore Q839Z1 Go to UniProtKB: Q839Z1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q839Z1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
DOO Query on DOO Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	6-fluoro-4-[(3aR,6aR)-hexahydropyrrolo[3,4-b]pyrrol-5(1H)-yl]-N-methyl-2-[(2-methylpyrimidin-5-yl)oxy]-9H-pyrimido[4,5-b]indol-8-amine C₂₂ H₂₃ F N₈ O ACMIJDVJWLMBCX-PXAZEXFGSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
TBU Query on TBU Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	TERTIARY-BUTYL ALCOHOL C₄ H₁₀ O DKGAVHZHDRPRBM-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.30 Å
R-Value Free: 0.196
R-Value Work: 0.178
R-Value Observed: 0.179
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.45	α = 90
b = 58.35	β = 90
c = 65.55	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2014-01-15

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2014-01-15
Type: Initial release
Version 1.1: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description

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Help and Resources

4K4O

The DNA Gyrase B ATP binding domain of Enterococcus faecalis in complex with a small molecule inhibitor

A new class of type IIA topoisomerase inhibitors with broad-spectrum antibacterial activity

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)