5BNM: E. coli FabH with Small Molecule Inhibitor 1

E. coli FabH with Small Molecule Inhibitor 1. Determined by X-ray diffraction at 1.7 Å resolution. Released 18 May 2016.

Method: X-ray diffraction
Resolution: 1.7 Å
Organism: Escherichia coli
Chains: 2
Atoms: 5,595
Mol. weight: 67.74 kDa
Ligands: 4VK
Released: 18 May 2016

Explore 5BNM in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5BNM contains 35 α-helices and 38 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: 17 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	2-11	10	1
β-strand	15-18	4	2
α-helix	19-25	7
α-helix	30-37	8
β-strand	41-44	4	2
α-helix	51-66	16
α-helix	70-72	3
β-strand	76-79	4	1
β-strand	85-87	3	3
α-helix	90-98	9
β-strand	102	1	4
β-strand	105-109	5	1
α-helix	111-113	3
α-helix	114-127	14
β-strand	133-140	8	1
α-helix	142-145	4
α-helix	151-154	4
β-strand	157	1	5
β-strand	160-169	10	1
β-strand	174-181	8	6
α-helix	183-185	3
β-strand	189-190	2	7
β-strand	191-192	2	8
β-strand	206-207	2	7
α-helix	209-230	22
α-helix	235-237	3
β-strand	240-243	4	6
α-helix	248-257	10
α-helix	262-264	3
β-strand	265	1	6
α-helix	269-272	4
β-strand	274	1	5
α-helix	276-278	3
α-helix	279-289	11
β-strand	298-305	8	6
β-strand	309-316	8	6

Chain B: 18 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	2-11	10	1
β-strand	15-18	4	9
α-helix	19-23	5
α-helix	30-37	8
β-strand	41-44	4	9
α-helix	51-66	16
α-helix	70-72	3
β-strand	76-79	4	1
β-strand	85-87	3	8
α-helix	90-98	9
β-strand	102	1	6
β-strand	105-109	5	1
α-helix	111-113	3
α-helix	114-127	14
β-strand	133-140	8	1
α-helix	142-145	4
α-helix	151-154	4
β-strand	157	1	10
β-strand	160-169	10	1
β-strand	174-181	8	4
α-helix	183-185	3
β-strand	189-190	2	11
β-strand	191-192	2	3
α-helix	193-194	2
β-strand	206-207	2	11
α-helix	209-230	22
α-helix	235-237	3
β-strand	240-243	4	4
α-helix	248-258	11
α-helix	262-264	3
β-strand	265	1	4
α-helix	269-272	4
β-strand	274	1	10
α-helix	276-278	3
α-helix	279-289	11
β-strand	298-305	8	4
β-strand	309-316	8	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
3-oxoacyl-[acyl-carrier-protein] synthase 3	A, B	protein	317	Escherichia coli	P0A6R0 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>5BNM_1 3-oxoacyl-[acyl-carrier-protein] synthase 3 (chains A, B)
MYTKIIGTGSYLPEQVRTNADLEKMVDTSDEWIVTRTGIRERHIAAPNETVSTMGFEAAT
RAIEMAGIEKDQIGLIVVATTSATHAFPSAACQIQSMLGIKGCPAFDVAAACAGFTYALS
VADQYVKSGAVKYALVVGSDVLARTCDPTDRGTIIIFGDGAGAAVLAASEEPGIISTHLH
ADGSYGELLTLPNADRVNPENSIHLTMAGNEVFKVAVTELAHIVDETLAANNLDRSQLDW
LVPHQANLRIISATAKKLGMSMDNVVVTLDRHGNTSAASVPCALDEAVRDGRIKPGQLVL
LEAFGGGFTWGSALVRF

Ligands and cofactors

ID	Name	Formula	Copies
4VK	N-{[3'-(hydroxymethyl)biphenyl-4-yl]methyl}benzenesulfonamide	C20 H19 N O3 S	1

Water and common crystallization additives (PG4, SO4) are not listed.

Primary citation

Antibacterial FabH Inhibitors with Mode of Action Validated in Haemophilus influenzae by in Vitro Resistance Mutation Mapping. McKinney, D.C., Eyermann, C.J., Gu, R.F. et al. ACS Infect Dis (2016) 2:456-464. DOI 10.1021/acsinfecdis.6b00053 · PubMed

Other PDB entries of the same protein (UniProt P0A6R0 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8D1U 1.3 Å, E. coli beta-ketoacyl-[acyl carrier protein] synthase III (FabH) with an acetylated…
6X7R 1.35 Å, E. coli beta-ketoacyl-[acyl carrier protein] synthase III (FabH) in complex with…
9KA5 1.42 Å, Crystal structure of beta-ketoacyl-ACP synthase FabH C112Q from E. coli
1HNJ 1.46 Å, Crystal structure of beta-ketoacyl-ACP synthase III + malonyl-CoA
9KA6 1.47 Å, Crystal structure of beta-ketoacyl-ACP synthase FabH C112Q in complex with acyl-ACP from…
9KA2 1.5 Å, Crystal structure of beta-ketoacyl-ACP synthase FabH from E. coli
1HND 1.6 Å, Crystal structure of beta-ketoacyl-ACP synthase III-CoA complex
1EBL 1.8 Å, The 1.8 a crystal structure and active site architecture of beta-ketoacyl-[acyl carrier…
3IL9 1.85 Å, Structure of E. coli FabH
5BNR 1.89 Å, E. coli Fabh with small molecule inhibitor 2
1HNH 1.9 Å, Crystal structure of beta-ketoacyl-ACP synthase III + degraded form of acetyl-CoA
1HNK 1.9 Å, Crystal structure of beta-ketoacyl-ACP synthase III, apo tetragonal form

Browse structure collections

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