7SZ9: 3-oxoacyl-[acyl-carrier-protein] synthase 1

Crosslinked Crystal Structure of Type II Fatty Acid Synthase Ketosynthase, FabB, and C16:1-crypto Acyl Carrier Protein, AcpP. Determined by X-ray diffraction at 2.2 Å resolution. Released 23 Nov 2022.

Method: X-ray diffraction
Resolution: 2.2 Å
Organisms: Escherichia coli (strain K12), Escherichia coli
Chains: 4
Atoms: 7,480
Mol. weight: 103.42 kDa
Ligands: DJ5
Released: 23 Nov 2022

Explore 7SZ9 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7SZ9 contains 55 α-helices and 60 β-strands across 4 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: 22 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	4-12	9	1
β-strand	13	1	2
β-strand	16	1	2
α-helix	19-28	10
β-strand	34-35	2	3
α-helix	37-41	5
β-strand	48-49	2	3
β-strand	50	1	4
α-helix	62-65	4
α-helix	70-86	17
α-helix	90-93	4
β-strand	99-105	7	1
α-helix	110-120	11
α-helix	126-128	3
α-helix	133-137	5
α-helix	141-147	7
β-strand	156-157	2	1
β-strand	158-160	3	5
α-helix	162-164	3
α-helix	165-178	14
β-strand	184-191	8	1
α-helix	195-204	10
β-strand	207	1	6
α-helix	215-217	3
β-strand	223	1	7
β-strand	229	1	6
α-helix	230	1
β-strand	231	1	8
β-strand	232	1	4
β-strand	234-242	9	1
α-helix	243-248	6
β-strand	255-264	10	1
α-helix	275-285	11
α-helix	291-292	2
β-strand	294-296	3	1
α-helix	305-317	13
α-helix	321-322	2
β-strand	323-325	3	1
α-helix	328-331	4
β-strand	333	1	8
α-helix	335-337	3
α-helix	338-352	15
β-strand	354-355	2	9
β-strand	364	1	7
β-strand	369	1	10
β-strand	371	1	10
β-strand	372-373	2	1
β-strand	378-379	2	9
β-strand	384-391	8	1
β-strand	395-402	8	1

Chain B: 24 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	4-12	9	11
β-strand	13	1	12
β-strand	16	1	12
α-helix	19-28	10
β-strand	34-35	2	13
α-helix	37-41	5
β-strand	48-49	2	13
β-strand	50	1	14
α-helix	62-65	4
α-helix	70-85	16
α-helix	90-93	4
β-strand	96	1	15
β-strand	99-104	6	11
α-helix	110-121	12
α-helix	125-128	4
α-helix	133-137	5
α-helix	141-147	7
β-strand	152	1	15
β-strand	156-157	2	11
β-strand	158-160	3	5
α-helix	162-164	3
α-helix	165-178	14
β-strand	184-191	8	11
α-helix	195-204	10
β-strand	207	1	16
α-helix	215-217	3
β-strand	223	1	17
β-strand	229	1	16
α-helix	230	1
β-strand	231	1	18
β-strand	232	1	14
β-strand	234-242	9	11
α-helix	243-248	6
α-helix	251-253	3
β-strand	255-264	10	11
α-helix	275-285	11
α-helix	291-292	2
β-strand	294-296	3	11
α-helix	305-317	13
α-helix	321-322	2
β-strand	323-325	3	11
α-helix	328-331	4
β-strand	333	1	18
α-helix	335-337	3
α-helix	338-352	15
β-strand	354-355	2	19
β-strand	364	1	17
α-helix	366-368	3
β-strand	372-373	2	11
β-strand	378-379	2	19
β-strand	384-391	8	11
β-strand	395-402	8	11

Chain C: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	7-15	9
β-strand	27	1	20
α-helix	36-49	14
α-helix	57-61	5
β-strand	64	1	20
α-helix	65-74	10

Chain D: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	3-15	13
α-helix	19-21	3
β-strand	27	1	21
α-helix	36-46	11
α-helix	56-59	4
β-strand	64	1	21
α-helix	65-74	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
3-oxoacyl-[acyl-carrier-protein] synthase 1	A, B	protein	406	Escherichia coli (strain K12)	P0A953 (AlphaFold model)
Acyl carrier protein	C, D	protein	77	Escherichia coli	P0A6A8 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>7SZ9_1 3-oxoacyl-[acyl-carrier-protein] synthase 1 (chains A, B)
VSKRAVITGLGIVSSIGNNQQEVLASLREGRSGITFSQELKDSGMRSHVWGNVKLDTTGL
IDRKVVRFMSDASIYAFLSMEQAIADAGLSPEAYQNNPRVGLIAGSGGGSPRFQVFGADA
MRGPRGLKAVGPYVVTKAMASGVSACLATPFKIHGVNYSISSACATSAHCIGNAVEQIQL
GKQDIVFAGGGEELCWEMACEFDAMGALSTKYNDTPEKASRTYDAHRDGFVIAGGGGMVV
VEELEHALARGAHIYAEIVGYGATSDGADMVAPSGEGAVRCMKMAMHGVDTPIDYLNSHG
TSTPVGDVKELAAIREVFGDKSPAISATKAMTGHSLGAAGVQEAIYSLLMLEHGFIAPSI
NIEELDEQAAGLNIVTETTDRELTTVMSNSFGFGGTNATLVMRKLK

Sequence of entity 2 (C, D), FASTA

>7SZ9_2 Acyl carrier protein (chains C, D)
STIEERVKKIIGEQLGVKQEEVTNNASFVEDLGADSLDTVELVMALEEEFDTEIPDEEAE
KITTVQAAIDYINGHQA

Ligands and cofactors

ID	Name	Formula	Copies
DJ5	N~3~-{(2R)-4-[(dihydroxyphosphanyl)oxy]-2-hydroxy-3,3-dimethylbutanoyl}-N-(2-{[…	C27 H52 N3 O8 P	2

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

Primary citation

Mechanism-based cross-linking probes capture the Escherichia coli ketosynthase FabB in conformationally distinct catalytic states. Chen, A., Mindrebo, J.T., Davis, T.D. et al. Acta Crystallogr D Struct Biol (2022) 78:1171-1179. DOI 10.1107/S2059798322007434 · PubMed

Other PDB entries of the same protein (UniProt P0A953 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2VBA 1.36 Å, beta-ketoacyl-ACP synthase I (KAS) from E. coli with bound amino- thiazole inhibitor
2VB9 1.5 Å, beta-ketoacyl-ACP synthase I (KAS) from E. coli, apo structure
2VB8 1.52 Å, beta-ketoacyl-ACP synthase I (KAS) from E. coli with bound inhibitor thiolactomycin
6OKC 1.55 Å, Crosslinked Crystal Structure of Type II Fatty Acid Synthase Ketosynthase, FabB, and…
2VB7 1.6 Å, beta-ketoacyl-ACP synthase I (KAS) from E. coli, apo structure after soak in PEG solution
2BYW 1.7 Å, Structure of Escherichia coli beta-ketoacyl (acyl carrier protein) synthase I LYS328ALA…
7SQI 1.7 Å, Crosslinked Crystal Structure of Type II Fatty Acid Synthase Ketosynthase, FabB, and…
1EK4 1.85 Å, Beta-ketoacyl [acyl carrier protein] synthase I in complex with dodecanoic acid to 1.85…
2BZ4 1.86 Å, structure of E.coli KAS I H298Q mutant
2BUH 1.9 Å, E. Coli beta-ketoacyl (acyl carrier protein) synthase I, 120 K
8SMS 1.93 Å, Crosslinked Crystal Structure of Type II Fatty Acid Synthase, FabB, and cerulenin…
2BYZ 1.95 Å, Structure of E.coli KAS I H298Q mutant in complex with C12 fatty acid

Browse structure collections

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