8D1U: 3-oxoacyl-[acyl-carrier-protein] synthase 3

Name: PDB 8D1U: E. coli beta-ketoacyl-[acyl carrier protein] synthase III (FabH) with an acetylated cysteine and in complex with oxa(dethia)-Coenzyme A
Published: 2022-06-15
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: transferase

E. coli beta-ketoacyl-[acyl carrier protein] synthase III (FabH) with an acetylated cysteine and in complex with oxa(dethia)-Coenzyme A. Determined by X-ray diffraction at 1.3 Å resolution. Released 15 Jun 2022.

Method: X-ray diffraction
Resolution: 1.3 Å
Organism: Escherichia coli
Chains: 1
Atoms: 3,081
Mol. weight: 34.58 kDa
Ligands: UT7
Released: 15 Jun 2022

Explore 8D1U in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8D1U contains 18 α-helices and 16 β-strands across 1 chain. 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, 16 β-strands

Element	Residues	Length	Sheet
β-strand	2-11	10	1
β-strand	15-18	4	2
α-helix	19-23	5
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
α-helix	90-98	9
β-strand	105-108	4	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	3
β-strand	160-169	10	1
β-strand	174-181	8	4
α-helix	183-188	6
β-strand	189-190	2	5
α-helix	192-194	3
β-strand	206-207	2	5
α-helix	209-230	22
α-helix	235-237	3
β-strand	240-243	4	4
α-helix	248-257	10
α-helix	262-264	3
β-strand	265	1	4
α-helix	269-272	4
β-strand	274	1	3
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	protein	320	Escherichia coli	P0A6R0 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>8D1U_1 3-oxoacyl-[acyl-carrier-protein] synthase 3 (chains A)
SGGMYTKIIGTGSYLPEQVRTNADLEKMVDTSDEWIVTRTGIRERHIAAPNETVSTMGFE
AATRAIEMAGIEKDQIGLIVVATTSATHAFPSAACQIQSMLGIKGCPAFDVAAACAGFTY
ALSVADQYVKSGAVKYALVVGSDVLARTCDPTDRGTIIIFGDGAGAAVLAASEEPGIIST
HLHADGSYGELLTLPNADRVNPENSIHLTMAGNEVFKVAVTELAHIVDETLAANNLDRSQ
LDWLVPHQANLRIISATAKKLGMSMDNVVVTLDRHGNTSAASVPCALDEAVRDGRIKPGQ
LVLLEAFGGGFTWGSALVRF

Ligands and cofactors

ID	Name	Formula	Copies
UT7	oxa(dethia)-CoA	C21 H36 N7 O17 P3	1

Water and common crystallization additives (CL) are not listed.

Primary citation

Structures of chloramphenicol acetyltransferase III and Escherichia coli beta-ketoacylsynthase III co-crystallized with partially hydrolysed acetyl-oxa(dethia)CoA. Benjamin, A.B., Stunkard, L.M., Ling, J. et al. Acta Crystallogr F Struct Biol Commun (2023) 79:61-69. DOI 10.1107/S2053230X23001206 · PubMed

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

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
1HNK 1.9 Å, Crystal structure of beta-ketoacyl-ACP synthase III, apo tetragonal form

Browse structure collections

About this viewer

MolViewer shows 8D1U 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.