3IL6 | pdb_00003il6

Structure of E. faecalis FabH in complex with 2-({4-[(3R,5S)-3,5-dimethylpiperidin-1-yl]-3-phenoxybenzoyl}amino)benzoic acid

PDB DOI: https://doi.org/10.2210/pdb3IL6/pdb

Classification: TRANSFERASE
Organism(s): Enterococcus faecalis
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2009-08-06 Released: 2009-08-25
Deposition Author(s): Gajiwala, K.S., Margosiak, S., Lu, J., Cortez, J., Su, Y., Nie, Z., Appelt, K.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.219 (Depositor), 0.194 (DCC)
R-Value Work:
0.185 (Depositor), 0.180 (DCC)
R-Value Observed:
0.190 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Crystal structures of bacterial FabH suggest a molecular basis for the substrate specificity of the enzyme.

Gajiwala, K.S., Margosiak, S., Lu, J., Cortez, J., Su, Y., Nie, Z., Appelt, K.

(2009) FEBS Lett 583: 2939-2946

PubMed: 19665020 Search on PubMed
DOI: https://doi.org/10.1016/j.febslet.2009.08.001
Primary Citation Related Structures:
3IL3, 3IL4, 3IL5, 3IL6, 3IL7, 3IL9

PubMed Abstract:
FabH (beta-ketoacyl-acyl carrier protein synthase III) is unique in that it initiates fatty acid biosynthesis, is inhibited by long-chain fatty acids providing means for feedback control of the process, and dictates the fatty acid profile of the organism by virtue of its substrate specificity. We report the crystal structures of bacterial FabH enzymes from four different pathogenic species: Enterococcus faecalis, Haemophilus influenzae, Staphylococcus aureus and Escherichia coli. Structural data on the enzyme from different species show important differences in the architecture of the substrate-binding sites that parallel the inter-species diversity in the substrate specificities of these enzymes.

Organizational Affiliation

Quorex Pharmaceuticals, Carlsbad, CA 92008, USA. ketan.gajiwala@pfizer.com

Macromolecule Content

Total Structure Weight: 36.21 kDa
Atom Count: 2,641
Modeled Residue Count: 320
Deposited Residue Count: 321
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-oxoacyl-[acyl-carrier-protein] synthase 3	A	321	Enterococcus faecalis	Mutation(s): 3 Gene Names: EF_2885, fabH EC: 2.3.1.180
UniProt
Find proteins for Q820T1 (Enterococcus faecalis (strain ATCC 700802 / V583)) Explore Q820T1 Go to UniProtKB: Q820T1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q820T1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
B83 Query on B83 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]	2-[({4-[(3R,5S)-3,5-dimethylpiperidin-1-yl]-3-phenoxyphenyl}carbonyl)amino]benzoic acid C₂₇ H₂₈ N₂ O₄ YMZMFFRGSWCLPY-KDURUIRLSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A]	C [auth A] D [auth A] E [auth A] F [auth A] G [auth A] C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A]