7UMW | pdb_00007umw

Crystal structure of E. Coli FabI in complex with NAD and Fabimycin ((S,E)-3-(7-amino-8-oxo-6,7,8,9-tetrahydro-5H-pyrido[2,3-b]azepin-3-yl)-N-methyl-N-((3-methylbenzofuran-2-yl)methyl)acrylamide)

PDB DOI: https://doi.org/10.2210/pdb7UMW/pdb

Classification: ANTIBIOTIC
Organism(s): Escherichia coli str. K-12 substr. MG1655
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2022-04-08 Released: 2022-12-14
Deposition Author(s): Hajian, B.
Funding Organization(s): Other private

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.54 Å
R-Value Free:
0.245 (Depositor), 0.244 (DCC)
R-Value Work:
0.213 (Depositor), 0.215 (DCC)
R-Value Observed:
0.214 (Depositor)

Starting Model: experimental
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Literature

An Iterative Approach Guides Discovery of the FabI Inhibitor Fabimycin, a Late-Stage Antibiotic Candidate with In Vivo Efficacy against Drug-Resistant Gram-Negative Infections

Parker, E.N., Cain, B.N., Hajian, B., Ulrich, R.J., Geddes, E.J., Barkho, S., Lee, H.Y., Williams, J.D., Raynor, M., Caridha, D., Zaino, A., Rohde, J.M., Zak, M., Shekhar, M., Munoz, K.A., Rzasa, K.M., Temple, E.R., Hunt, D., Jin, X., Vuong, C., Pannone, K., Kelly, A.M., Mulligan, M.P., Lee, K.K., Lau, G.W., Hung, D.T., Hergenrother, P.J.

(2022) ACS Cent Sci 8: 1362-1362

PubMed: 36188352 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1021/acscentsci.2c00969
Primary Citation Related Structures:
7UM8, 7UMW, 7UMX, 7UMY

PubMed Abstract:
[This corrects the article DOI: 10.1021/acscentsci.2c00598.].

Organizational Affiliation

Department of Chemistry and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.

Macromolecule Content

Total Structure Weight: 58.66 kDa
Atom Count: 4,344
Modeled Residue Count: 519
Deposited Residue Count: 532
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Enoyl-[acyl-carrier-protein] reductase [NADH] FabI	A, B	266	Escherichia coli str. K-12 substr. MG1655	Mutation(s): 0 Gene Names: fabI EC: 1.3.1.9
UniProt
Find proteins for P0AEK4 (Escherichia coli (strain K12)) Explore P0AEK4 Go to UniProtKB: P0AEK4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0AEK4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAD Query on NAD Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain E [auth B] MOL2 format, chain C [auth A] MOL2 format, chain E [auth B] mmCIF format, chain C [auth A] mmCIF format, chain E [auth B]	C [auth A], E [auth B]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]
NUC (Subject of Investigation/LOI) Query on NUC 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]	(2E)-3-[(7S)-7-amino-8-oxo-6,7,8,9-tetrahydro-5H-pyrido[2,3-b]azepin-3-yl]-N-methyl-N-[(3-methyl-1-benzofuran-2-yl)methyl]prop-2-enamide C₂₃ H₂₄ N₄ O₃ ZWQNEFFHBSGFHV-HKMNZKMDSA-N		Interactions Focus chain D [auth A] Focus chain F [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.54 Å
R-Value Free: 0.245 (Depositor), 0.244 (DCC)
R-Value Work: 0.213 (Depositor), 0.215 (DCC)
R-Value Observed: 0.214 (Depositor)

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.54	α = 90
b = 79.54	β = 90
c = 323.68	γ = 120

Software Package:

Software Name	Purpose
Aimless	data scaling
PHENIX	refinement
XDS	data reduction
Coot	model building
PDB_EXTRACT	data extraction
PHENIX	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2022-12-14

Deposition Author(s):

Funding Organization	Location	Grant Number
Other private	United States	--

Revision History (Full details and data files)

Version 1.0: 2022-12-14
Type: Initial release
Version 1.1: 2023-02-15
Changes: Database references
Version 1.2: 2023-08-16
Changes: Data collection, Source and taxonomy
Version 1.3: 2023-10-25
Changes: Refinement description

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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.