6C55 | pdb_00006c55

Crystal structure of Staphylococcus aureus Ketol-acid Reductosimerrase with hydroxyoxamate inhibitor 3

PDB DOI: https://doi.org/10.2210/pdb6C55/pdb

Classification: OXIDOREDUCTASE
Organism(s): Staphylococcus aureus RF122
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2018-01-14 Released: 2019-01-16
Deposition Author(s): Kandale, A., Patel, K.M., Zheng, S., You, L., Guddat, L.W., Schenk, G., Schmbri, M., McGeary, R.P.
Funding Organization(s): National Health and Medical Research Council (NHMRC, Australia)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.09 Å
R-Value Free:
0.206 (Depositor), 0.207 (DCC)
R-Value Work:
0.163 (Depositor), 0.165 (DCC)
R-Value Observed:
0.165 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Design, synthesis, in vitro activity and crystallisation of novel N-isopropyl-N-hydroxyoxamate derivatives as ketol-acid reductoisomerase (KARI) inhibitors

Kandale, A., Patel, K.M., Zheng, S., You, L., Guddat, L.W., Schenk, G., Schmbri, M., McGeary, R.P.

To be published.

Macromolecule Content

Total Structure Weight: 77.89 kDa
Atom Count: 5,590
Modeled Residue Count: 652
Deposited Residue Count: 680
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ketol-acid reductoisomerase (NADP(+))	A, B	340	Staphylococcus aureus RF122	Mutation(s): 0 Gene Names: ilvC, SAB1941 EC: 1.1.1.86
UniProt
Find proteins for Q2YUF3 (Staphylococcus aureus (strain bovine RF122 / ET3-1)) Explore Q2YUF3 Go to UniProtKB: Q2YUF3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q2YUF3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAP Query on NAP Download:Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain E [auth A] MOL2 format, chain K [auth B] MOL2 format, chain E [auth A] mmCIF format, chain K [auth B] mmCIF format, chain E [auth A]	E [auth A], K [auth B]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₂₈ N₇ O₁₇ P₃ XJLXINKUBYWONI-NNYOXOHSSA-N		Interactions Focus chain E [auth A] Focus chain K [auth B] Interactions & Density Focus chain E [auth A] Focus chain K [auth B]
EKA Query on EKA Download:Ideal Coordinates CCD File SDF format, chain I [auth A] MOL2 format, chain I [auth A] mmCIF format, chain I [auth A]	I [auth A]	[cyclohexyl(hydroxy)amino](oxo)acetic acid C₈ H₁₃ N O₄ HMDGECZILRJLEV-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Interactions & Density Focus chain I [auth A]
EKD Query on EKD Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain H [auth A] MOL2 format, chain F [auth A] MOL2 format, chain H [auth A] mmCIF format, chain F [auth A] mmCIF format, chain H [auth A]	F [auth A], H [auth A]	(cyclohexylamino)(oxo)acetic acid C₈ H₁₃ N O₃ JXKXKOUBASQQOF-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain H [auth A] Interactions & Density Focus chain F [auth A] Focus chain H [auth A]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain G [auth A] SDF format, chain J [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain G [auth A] MOL2 format, chain J [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain G [auth A] mmCIF format, chain J [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth A], G [auth A], J [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain G [auth A] Focus chain J [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain G [auth A] Focus chain J [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.09 Å
R-Value Free: 0.206 (Depositor), 0.207 (DCC)
R-Value Work: 0.163 (Depositor), 0.165 (DCC)
R-Value Observed: 0.165 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.724	α = 90
b = 79.032	β = 101.39
c = 69.64	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2019-01-16

Deposition Author(s):

Funding Organization	Location	Grant Number
National Health and Medical Research Council (NHMRC, Australia)	Australia	--

Revision History (Full details and data files)

Version 1.0: 2019-01-16
Type: Initial release
Version 1.1: 2020-01-08
Changes: Author supporting evidence
Version 1.2: 2023-10-04
Changes: Data collection, Database references, Derived calculations, Refinement description

6C55 | pdb_00006c55

Crystal structure of Staphylococcus aureus Ketol-acid Reductosimerrase with hydroxyoxamate inhibitor 3

Literature

Design, synthesis, in vitro activity and crystallisation of novel N-isopropyl-N-hydroxyoxamate derivatives as ketol-acid reductoisomerase (KARI) inhibitors

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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