6BUL | pdb_00006bul

Crystal structure of Staphylococcus aureus ketol-acid reductoisomerase with hydroxyoxamate inhibitor 2

PDB DOI: https://doi.org/10.2210/pdb6BUL/pdb

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

Deposited: 2017-12-10 Released: 2018-12-12
Deposition Author(s): Kandale, A., Patel, K.M., Zheng, S., You, L., Guddat, L.W., Schenk, G., Schembri, M.A., McFeary, R.P.
Funding Organization(s): National Health and Medical Research Council (NHMRC, Australia)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.88 Å
R-Value Free:
0.209 (Depositor), 0.210 (DCC)
R-Value Work:
0.163 (Depositor), 0.160 (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 2.1 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., Schembri, M.A., McFeary, R.P.

To be published.

Macromolecule Content

Total Structure Weight: 78.16 kDa
Atom Count: 5,584
Modelled Residue Count: 648
Deposited Residue Count: 680
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q2YUF3
Sequence Annotations Expand
Reference Sequence LOADING

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 E [auth A] SDF format, chain L [auth B] MOL2 format, chain E [auth A] MOL2 format, chain L [auth B] mmCIF format, chain E [auth A] mmCIF format, chain L [auth B]	E [auth A], L [auth B]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₂₈ N₇ O₁₇ P₃ XJLXINKUBYWONI-NNYOXOHSSA-N		Interactions Focus chain E [auth A] Focus chain L [auth B] Interactions & Density Focus chain E [auth A] Focus chain L [auth B]
E9G Query on E9G Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain H [auth B] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] mmCIF format, chain F [auth A] mmCIF format, chain H [auth B]	F [auth A], H [auth B]	{hydroxy[(1S)-1-phenylethyl]amino}(oxo)acetic acid C₁₀ H₁₁ N O₄ IRVSUCQNKPWMLV-ZETCQYMHSA-N		Interactions Focus chain F [auth A] Focus chain H [auth B] Interactions & Density Focus chain F [auth A] Focus chain H [auth B]
E9J Query on E9J Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain I [auth B] MOL2 format, chain G [auth A] MOL2 format, chain I [auth B] mmCIF format, chain G [auth A] mmCIF format, chain I [auth B]	G [auth A], I [auth B]	oxo{[(1S)-1-phenylethyl]amino}acetic acid C₁₀ H₁₁ N O₃ RVIXKSXCAWSWSX-ZETCQYMHSA-N		Interactions Focus chain G [auth A] Focus chain I [auth B] Interactions & Density Focus chain G [auth A] Focus chain I [auth B]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth A], J [auth B], K [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain J [auth B] Focus chain K [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain J [auth B] Focus chain K [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.88 Å
R-Value Free: 0.209 (Depositor), 0.210 (DCC)
R-Value Work: 0.163 (Depositor), 0.160 (DCC)
R-Value Observed: 0.165 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.825	α = 90
b = 78.912	β = 101.1
c = 69.37	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

Entry History & Funding Information

Deposition Data

Released Date: 2018-12-12

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: 2018-12-12
Type: Initial release
Version 1.1: 2020-01-08
Changes: Author supporting evidence
Version 2.0: 2021-11-24
Changes: Atomic model, Database references, Derived calculations
Version 2.1: 2023-10-04
Changes: Data collection, Refinement description

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Crystal structure of Staphylococcus aureus ketol-acid reductoisomerase with hydroxyoxamate inhibitor 2

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

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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