8SMS: 3-oxoacyl-[acyl-carrier-protein] synthase 1

Crosslinked Crystal Structure of Type II Fatty Acid Synthase, FabB, and cerulenin crosslinker-crypto Acyl Carrier Protein, AcpP. Determined by X-ray diffraction at 1.93 Å resolution. Released 27 Sept 2023.

Method: X-ray diffraction
Resolution: 1.93 Å
Organisms: Escherichia coli K-12, Atlantibacter hermannii NBRC 105704
Chains: 4
Atoms: 7,603
Mol. weight: 103.33 kDa
Ligands: G7U
Released: 27 Sept 2023

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

Secondary structure: helices and β-sheets

8SMS contains 49 α-helices and 59 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: 20 helices, 30 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	37-42	6
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	96	1	5
β-strand	99-104	6	1
α-helix	110-120	11
α-helix	126-129	4
α-helix	133-137	5
α-helix	141-147	7
β-strand	152	1	5
β-strand	156-157	2	1
β-strand	158-160	3	6
β-strand	161	1	7
β-strand	163	1	7
α-helix	165-178	14
β-strand	184-191	8	1
α-helix	195-202	8
β-strand	207	1	8
α-helix	215-217	3
β-strand	223	1	9
β-strand	229	1	8
β-strand	231	1	10
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
β-strand	294-296	3	1
α-helix	303-317	15
α-helix	321-322	2
β-strand	323-325	3	1
α-helix	328-331	4
β-strand	333	1	10
α-helix	335-337	3
α-helix	338-352	15
β-strand	354-355	2	11
β-strand	364	1	9
α-helix	366-368	3
β-strand	372-373	2	1
β-strand	378-379	2	11
β-strand	384-391	8	1
β-strand	395-402	8	1

Chain B: 21 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	4-12	9	12
β-strand	13	1	13
β-strand	16	1	13
α-helix	19-28	10
β-strand	33-35	3	14
α-helix	37-42	6
β-strand	48-50	3	14
α-helix	62-65	4
α-helix	70-85	16
α-helix	90-93	4
β-strand	99-104	6	12
α-helix	110-120	11
α-helix	126-129	4
α-helix	133-137	5
α-helix	141-147	7
β-strand	156-157	2	12
β-strand	158-160	3	6
β-strand	161	1	15
β-strand	163	1	15
α-helix	165-178	14
β-strand	184-191	8	12
α-helix	195-203	9
β-strand	207	1	16
α-helix	215-218	4
β-strand	229	1	16
β-strand	231	1	17
β-strand	232	1	14
β-strand	234-242	9	12
α-helix	243-248	6
β-strand	255-264	10	12
α-helix	275-285	11
β-strand	294-296	3	12
α-helix	303-316	14
β-strand	323-325	3	12
α-helix	328-331	4
β-strand	333	1	17
α-helix	335-337	3
α-helix	338-351	14
β-strand	354-355	2	18
α-helix	356-358	3
α-helix	366-368	3
β-strand	372-373	2	12
β-strand	378-379	2	18
β-strand	384-391	8	12
α-helix	392-394	3
β-strand	395-402	8	12

Chain C: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	6-16	11
β-strand	27	1	19
α-helix	36-50	15
α-helix	56-59	4
β-strand	64	1	19
α-helix	65-74	10

Chain D: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	3-15	13
β-strand	27	1	20
α-helix	36-50	15
α-helix	56-61	6
β-strand	64	1	20
α-helix	65-73	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
3-oxoacyl-[acyl-carrier-protein] synthase 1	A, B	protein	406	Escherichia coli K-12	P0A953 (AlphaFold model)
Acyl carrier protein	C, D	protein	77	Atlantibacter hermannii NBRC 105704	H5V184 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>8SMS_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

>8SMS_2 Acyl carrier protein (chains C, D)
STIEERVKKIIGEQLGVKQEEVTNNASFVEDLGADSLDTVELVMALEEEFDTEIPDEEAE
KITTVQAAIDYINGHQA

Ligands and cofactors

ID	Name	Formula	Copies
G7U	N~3~-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-N-{2-[(2R)-2-hydrox…	C23 H44 N3 O10 P	2

Primary citation

Masked cerulenin enables a dual-site selective protein crosslink. Jiang, Z., Chen, A., Chen, J. et al. Chem Sci (2023) 14:10925-10933. DOI 10.1039/d3sc02864j · 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
2BYZ 1.95 Å, Structure of E.coli KAS I H298Q mutant in complex with C12 fatty acid
1H4F 2.0 Å, E. Coli beta-ketoacyl [acyl carrier protein] synthase I K328R

Browse structure collections

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