4OKG | pdb_00004okg

LpxC from P.aeruginosa with the inhibitor 6-(benzimidazol-1-yl)-5-[4-[2-[6-[(4-methylpiperazin-1-yl)methyl]-3-pyridyl]ethynyl]phenyl]pyridine-3-carbohydroxamic acid

PDB DOI: https://doi.org/10.2210/pdb4OKG/pdb

Classification: HYDROLASE/HYDROLASE INHIBITOR
Organism(s): Pseudomonas aeruginosa PAO1
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2014-01-22 Released: 2014-09-24
Deposition Author(s): Olivier, N.B., Lahiri, S.D., Prince, D.B.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.06 Å
R-Value Free:
0.219 (Depositor), 0.221 (DCC)
R-Value Work:
0.167 (Depositor), 0.169 (DCC)
R-Value Observed:
0.169 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 4OKG

Ligand Structure Quality Assessment

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

Literature

Overexpression of Pseudomonas aeruginosa LpxC in the Presence of an Inhibitor in an acrB Deletion Escherichia coli strain for Structural Studies

Gao, N., McLeod, S.M., Hajec, H., Lahiri, S.D., Prince, D.B., Thresher, J., Whiteaker, J., Ross, P., Olivier, N.B., Doig, P.

(2014) Protein Express Purif

Macromolecule Content

Total Structure Weight: 67.51 kDa
Atom Count: 5,058
Modeled Residue Count: 590
Deposited Residue Count: 598
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase	A, B	299	Pseudomonas aeruginosa PAO1	Mutation(s): 1 Gene Names: envA, lpxC, PA4406 EC: 3.5.1 (PDB Primary Data), 3.5.1.108 (UniProt)
UniProt
Find proteins for P47205 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore P47205 Go to UniProtKB: P47205
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P47205
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
2SZ Query on 2SZ Download:Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain D [auth A] MOL2 format, chain F [auth B] MOL2 format, chain D [auth A] mmCIF format, chain F [auth B] mmCIF format, chain D [auth A]	D [auth A], F [auth B]	6-(1H-benzimidazol-1-yl)-N-hydroxy-5-[4-({6-[(4-methylpiperazin-1-yl)methyl]pyridin-3-yl}ethynyl)phenyl]pyridine-3-carboxamide C₃₂ H₂₉ N₇ O₂ YJCPLYNHCKYCMY-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain F [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth B]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain E [auth B] SDF format, chain C [auth A] MOL2 format, chain E [auth B] MOL2 format, chain C [auth A] mmCIF format, chain E [auth B] mmCIF format, chain C [auth A]	C [auth A], E [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.06 Å
R-Value Free: 0.219 (Depositor), 0.221 (DCC)
R-Value Work: 0.167 (Depositor), 0.169 (DCC)
R-Value Observed: 0.169 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 35.77	α = 90
b = 157.115	β = 101.87
c = 48.946	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
BUSTER-TNT	refinement
PDB_EXTRACT	data extraction
StructureStudio	data collection
PHASES	phasing
BUSTER	refinement

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2014-09-24

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2014-09-24
Type: Initial release
Version 1.1: 2024-02-28
Changes: Data collection, Database references, Derived calculations

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.