7UMW: E. Coli FabI

Name: PDB 7UMW: 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)
Published: 2022-12-14
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: antibiotic

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). Determined by X-ray diffraction at 1.54 Å resolution. Released 14 Dec 2022.

Method: X-ray diffraction
Resolution: 1.54 Å
Organism: Escherichia coli str. K-12 substr. MG1655
Chains: 2
Atoms: 4,344
Mol. weight: 58.66 kDa
Ligands: NUC, NAD
Released: 14 Dec 2022

Explore 7UMW in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7UMW contains 37 α-helices and 16 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 18 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	8-11	4	1
α-helix	20-30	11
β-strand	34-39	6	1
α-helix	42-54	13
β-strand	60-62	3	1
α-helix	68-79	12
β-strand	85-90	6	1
α-helix	97-100	4
α-helix	104-107	4
α-helix	110-117	8
α-helix	118-122	5
α-helix	123-131	9
α-helix	132-134	3
β-strand	135-145	11	1
α-helix	147-149	3
α-helix	158-177	20
α-helix	178-180	3
β-strand	182-189	8	1
α-helix	190-191	2
α-helix	195-197	3
α-helix	203-213	11
α-helix	222-232	11
α-helix	235-237	3
β-strand	244-247	4	1
α-helix	251-253	3

Chain B: 19 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	8-11	4	2
α-helix	20-30	11
β-strand	34-39	6	2
α-helix	42-44	3
α-helix	45-54	10
β-strand	60-62	3	2
α-helix	68-79	12
β-strand	85	1	3
β-strand	88-90	3	2
α-helix	97-100	4
α-helix	104-107	4
α-helix	110-117	8
α-helix	118-122	5
α-helix	123-131	9
α-helix	132-134	3
β-strand	135	1	3
α-helix	136	1
β-strand	139-145	7	2
α-helix	147-149	3
α-helix	158-177	20
β-strand	182-189	8	2
α-helix	190-191	2
α-helix	195-197	3
α-helix	203-213	11
α-helix	222-232	11
α-helix	235-237	3
β-strand	244-247	4	2
α-helix	251-253	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Enoyl-[acyl-carrier-protein] reductase [NADH] FabI	A, B	protein	266	Escherichia coli str. K-12 substr. MG1655	P0AEK4 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>7UMW_1 Enoyl-[acyl-carrier-protein] reductase [NADH] FabI (chains A, B)
GDHGMGFLSGKRILVTGVASKLSIAYGIAQAMHREGAELAFTYQNDKLKGRVEEFAAQLG
SDIVLQCDVAEDASIDTMFAELGKVWPKFDGFVHSIGFAPGDQLDGDYVNAVTREGFKIA
HDISSYSFVAMAKACRSMLNPGSALLTLSYLGAERAIPNYNVMGLAKASLEANVRYMANA
MGPEGVRVNAISAGPIRTLAASGIKDFRKMLAHCEAVTPIRRTVTIEDVGNSAAFLCSDL
SAGISGEVVHVDGGFSIAAMNELELK

Ligands and cofactors

ID	Name	Formula	Copies
NUC	(2E)-3-[(7S)-7-amino-8-oxo-6,7,8,9-tetrahydro-5H-pyrido[2,3-b]azepin-3-yl]-N-me…	C23 H24 N4 O3	2
NAD	Nicotinamide-adenine-dinucleotide	C21 H27 N7 O14 P2	2

Primary citation

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. et al. ACS Cent Sci (2022) 8:1362-1362. DOI 10.1021/acscentsci.2c00969 · PubMed

Other PDB entries of the same protein (UniProt P0AEK4 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7UM8 1.7 Å, Crystal structure of E. Coli FabI in complex with NAD and…
1QSG 1.75 Å, Crystal structure of enoyl reductase inhibition by triclosan
4CV2 1.8 Å, Crystal structure of E. coli FabI in complex with NADH and CG400549
1QG6 1.9 Å, Crystal structure of E. Coli enoyl acyl carrier protein reductase in complex with NAD…
3PJF 1.9 Å, Structure of ENR G93V mutant-NAD+-triclosan complex
4CV3 1.95 Å, Crystal structure of E. coli FabI in complex with NADH and PT166
5CFZ 1.97 Å, Crystal structure of E. coli FabI in apo form
1C14 2.0 Å, Crystal structure of E coli enoyl reductase-NAD+-triclosan complex
4D46 2.0 Å, Crystal structure of E. coli FabI in complex with NAD and…
5CG1 2.07 Å, Crystal structure of E. coli FabI bound to the carbamoylated benzodiazaborine inhibitor…
1DFI 2.09 Å, X-ray structure of escherichia coli enoyl reductase with bound NAD
5CG2 2.11 Å, Crystal structure of E. coli FabI bound to the thiocarbamoylated benzodiazaborine…

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