4FW4 | pdb_00004fw4

Crystal Structure of the LpxC in complex with N-[(1S,2R)-2-HYDROXY-1-(HYDROXYCARBAMOYL)PROPYL]-4-(4-PHENYLBUTA-1,3-DIYN-1-YL)BENZAMIDE inhibitor

PDB DOI: https://doi.org/10.2210/pdb4FW4/pdb

Classification: Hydrolase/Hydrolase Inhibitor
Organism(s): Pseudomonas aeruginosa PAO1
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2012-06-29 Released: 2013-05-15
Deposition Author(s): Kang, Y.N., Stuckey, J.A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.19 Å
R-Value Free:
0.223 (Depositor), 0.213 (DCC)
R-Value Work:
0.185 (Depositor), 0.178 (DCC)
R-Value Observed:
0.187 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal Structure of the LpxC

Kang, Y.N., Stuckey, J.A.

To be published.

Macromolecule Content

Total Structure Weight: 135.72 kDa
Atom Count: 9,819
Modeled Residue Count: 1,204
Deposited Residue Count: 1,208
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase	A, B, C, D	302	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 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
3P3 Query on 3P3 Download:Ideal Coordinates CCD File SDF format, chain O [auth D] SDF format, chain K [auth C] SDF format, chain H [auth B] SDF format, chain F [auth A] MOL2 format, chain O [auth D] MOL2 format, chain K [auth C] MOL2 format, chain H [auth B] MOL2 format, chain F [auth A] mmCIF format, chain O [auth D] mmCIF format, chain K [auth C] mmCIF format, chain H [auth B] mmCIF format, chain F [auth A]	F [auth A], H [auth B], K [auth C], O [auth D]	N-[(1S,2R)-2-hydroxy-1-(hydroxycarbamoyl)propyl]-4-(4-phenylbuta-1,3-diyn-1-yl)benzamide C₂₁ H₁₈ N₂ O₄ VUYMSCCEGRLBAF-BEFAXECRSA-N		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain K [auth C] Focus chain O [auth D] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain K [auth C] Focus chain O [auth D]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain P [auth D] SDF format, chain L [auth C] SDF format, chain I [auth B] MOL2 format, chain P [auth D] MOL2 format, chain L [auth C] MOL2 format, chain I [auth B] mmCIF format, chain P [auth D] mmCIF format, chain L [auth C] mmCIF format, chain I [auth B]	I [auth B], L [auth C], P [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain I [auth B] Focus chain L [auth C] Focus chain P [auth D] Interactions & Density Focus chain I [auth B] Focus chain L [auth C] Focus chain P [auth D]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain N [auth D] SDF format, chain J [auth C] SDF format, chain G [auth B] SDF format, chain E [auth A] MOL2 format, chain N [auth D] MOL2 format, chain J [auth C] MOL2 format, chain G [auth B] MOL2 format, chain E [auth A] mmCIF format, chain N [auth D] mmCIF format, chain J [auth C] mmCIF format, chain G [auth B] mmCIF format, chain E [auth A]	E [auth A], G [auth B], J [auth C], N [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain J [auth C] Focus chain N [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain J [auth C] Focus chain N [auth D]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain M [auth C] MOL2 format, chain M [auth C] mmCIF format, chain M [auth C]	M [auth C]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain M [auth C] Interactions & Density Focus chain M [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.19 Å
R-Value Free: 0.223 (Depositor), 0.213 (DCC)
R-Value Work: 0.185 (Depositor), 0.178 (DCC)
R-Value Observed: 0.187 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 35.674	α = 90
b = 89.332	β = 90
c = 170.674	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
BUSTER-TNT	refinement
PDB_EXTRACT	data extraction
MD2	data collection
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing
BUSTER	refinement

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2013-05-15

Deposition Author(s):

Kang, Y.N.

Stuckey, J.A.

Revision History (Full details and data files)

Version 1.0: 2013-05-15
Type: Initial release
Version 1.1: 2017-11-15
Changes: Refinement description
Version 1.2: 2024-02-28
Changes: Data collection, Database references, Derived calculations

4FW4 | pdb_00004fw4

Crystal Structure of the LpxC in complex with N-[(1S,2R)-2-HYDROXY-1-(HYDROXYCARBAMOYL)PROPYL]-4-(4-PHENYLBUTA-1,3-DIYN-1-YL)BENZAMIDE inhibitor

Literature

Crystal Structure of the LpxC

Biological Assembly 1

Biological Assembly 2

Biological Assembly 3

Biological Assembly 4

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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