4KTN | pdb_00004ktn

Dna gyrase atp binding domain of enterococcus faecalis in complex with a small molecule inhibitor ((3S)-1-[2-(PYRIDO[2,3-B]PYRAZIN-7-YLSULFANYL)-9H-PYRIMIDO[4,5-B]INDOL-4-YL]PYRROLIDIN-3-AMINE)

PDB DOI: https://doi.org/10.2210/pdb4KTN/pdb

Classification: Isomerase/isomerase inhibitor
Organism(s): Enterococcus faecalis V583
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2013-05-20 Released: 2014-01-15
Deposition Author(s): Bensen, D.C., Akers-rodriguez, S., Tari, L.W.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.69 Å
R-Value Free:
0.203 (Depositor), 0.210 (DCC)
R-Value Work:
0.173 (Depositor), 0.170 (DCC)
R-Value Observed:
0.174 (Depositor)

wwPDB Validation 3D Report Full Report

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: 24.25 kDa
Atom Count: 1,818
Modeled Residue Count: 193
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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MJU Query on MJU 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]	(3S)-1-[2-(pyrido[2,3-b]pyrazin-7-ylsulfanyl)-9H-pyrimido[4,5-b]indol-4-yl]pyrrolidin-3-amine C₂₁ H₁₈ N₈ S YQQNXOBXIZYKPR-LBPRGKRZSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.69 Å
R-Value Free: 0.203 (Depositor), 0.210 (DCC)
R-Value Work: 0.173 (Depositor), 0.170 (DCC)
R-Value Observed: 0.174 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.797	α = 90
b = 58.952	β = 90
c = 65.937	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):

Akers-rodriguez, S.

Revision History (Full details and data files)

Version 1.0: 2014-01-15
Type: Initial release
Version 1.1: 2024-02-28
Changes: Data collection, Database references, Derived calculations

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.