9KA7: Beta-ketoacyl-ACP synthase FabH C112Q

Crystal structure of beta-ketoacyl-ACP synthase FabH C112Q in complex with malonyl-ACP from E. coli. Determined by X-ray diffraction at 2.3 Å resolution. Released 10 Sept 2025.

Method: X-ray diffraction
Resolution: 2.3 Å
Organism: Escherichia coli
Chains: 3
Atoms: 5,743
Mol. weight: 81.61 kDa
Ligands: A1EE0
Released: 10 Sept 2025

Explore 9KA7 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9KA7 contains 40 α-helices and 42 β-strands across 3 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, 21 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	75-79	5	1
β-strand	85-87	3	3
α-helix	90-97	8
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
β-strand	146	1	5
α-helix	151-154	4
β-strand	157	1	6
β-strand	160-169	10	1
β-strand	174-181	8	7
α-helix	183-188	6
β-strand	189-190	2	8
β-strand	191-192	2	9
β-strand	205	1	5
β-strand	206-207	2	8
α-helix	209-230	22
α-helix	235-237	3
β-strand	240-243	4	7
α-helix	248-258	11
α-helix	262-264	3
β-strand	265	1	7
α-helix	269-272	4
β-strand	274	1	6
α-helix	276-278	3
α-helix	279-289	11
β-strand	298-305	8	7
β-strand	309-316	8	7

Chain B: 18 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	2-11	10	1
β-strand	15-18	4	10
α-helix	19-25	7
α-helix	30-37	8
β-strand	41-44	4	10
α-helix	51-66	16
α-helix	70-72	3
β-strand	76-79	4	1
β-strand	85-87	3	9
α-helix	90-97	8
β-strand	102	1	7
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	11
β-strand	160-169	10	1
β-strand	174-181	8	4
α-helix	183-188	6
β-strand	189-190	2	12
β-strand	191-192	2	3
α-helix	193-194	2
β-strand	206-207	2	12
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	11
α-helix	276-278	3
α-helix	279-289	11
β-strand	298-305	8	4
β-strand	309-316	8	4

Chain C: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	3-15	13
α-helix	19-21	3
β-strand	27	1	13
α-helix	36-50	15
α-helix	56-59	4
β-strand	64	1	13
α-helix	65-74	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Beta-ketoacyl-[acyl-carrier-protein] synthase III	A, B	protein	337	Escherichia coli	P0A6R0 (AlphaFold model)
Acyl carrier protein	C	protein	86	Escherichia coli	P0A6A8 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>9KA7_1 Beta-ketoacyl-[acyl-carrier-protein] synthase III (chains A, B)
MGSSHHHHHHSSGLVPRGSHMYTKIIGTGSYLPEQVRTNADLEKMVDTSDEWIVTRTGIR
ERHIAAPNETVSTMGFEAATRAIEMAGIEKDQIGLIVVATTSATHAFPSAACQIQSMLGI
KGCPAFDVAAAQAGFTYALSVADQYVKSGAVKYALVVGSDVLARTCDPTDRGTIIIFGDG
AGAAVLAASEEPGIISTHLHADGSYGELLTLPNADRVNPENSIHLTMAGNEVFKVAVTEL
AHIVDETLAANNLDRSQLDWLVPHQANLRIISATAKKLGMSMDNVVVTLDRHGNTSAASV
PCALDEAVRDGRIKPGQLVLLEAFGGGFTWGSALVRF

Sequence of entity 2 (C), FASTA

>9KA7_2 Acyl carrier protein (chains C)
SHMTIEERVKKIIGEQLGVKQEEVTNNASFVEDLGADSLDTVELVMALEEEFDTEIPDEE
AEKITTVQAAIDYINGHQASHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
A1EE0	3-[2-[3-[[(2R)-4-bis(oxidanyl)phosphanyloxy-3,3-dimethyl-2-oxidanyl-butanoyl]am…	C14 H25 N2 O9 P S	1

Primary citation

The Molecular Basis of the beta-Ketoacyl-ACP Synthase FabH in Catalyzing C-C Bond Formation of Acetoacetyl-ACP. Cai, C., Huang, Y., Zhang, L. et al. ACS Catal (2025) 15:5028-5038. DOI 10.1021/acscatal.5c01167

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
5BNM 1.7 Å, E. coli FabH with Small Molecule Inhibitor 1
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

Browse structure collections

About this viewer

MolViewer shows 9KA7 directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.