9N50: PDB entry 9N50

Crosslinked Crystal Structure of Human Mitochondrial Ketosynthase, OXSM, and Crosslinker-crypto Human Mitochondrial Acyl Carrier Protein, C8aBr-mACP. Determined by X-ray diffraction at 2.5 Å resolution. Released 24 Sept 2025.

Method: X-ray diffraction
Resolution: 2.5 Å
Organism: Homo sapiens
Chains: 3
Atoms: 6,973
Mol. weight: 100.45 kDa
Ligands: A1BMZ
Released: 24 Sept 2025

Explore 9N50 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9N50 contains 49 α-helices and 50 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: 22 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	44-53	10	1
β-strand	56-57	2	1
α-helix	59-68	10
β-strand	73-75	3	2
α-helix	80-83	4
β-strand	88-90	3	2
β-strand	94	1	3
β-strand	101	1	3
α-helix	103-106	4
α-helix	109-114	6
α-helix	117-133	17
α-helix	140-145	6
β-strand	146-152	7	1
α-helix	157-170	14
α-helix	172-174	3
α-helix	179-183	5
α-helix	187-196	10
β-strand	202	1	1
β-strand	207	1	4
β-strand	209	1	4
α-helix	211-225	15
β-strand	230-237	8	1
α-helix	242-250	9
β-strand	254	1	5
β-strand	274	1	5
β-strand	276	1	6
β-strand	279-287	9	1
α-helix	288-293	6
β-strand	300-309	10	1
α-helix	322-335	14
α-helix	339-341	3
β-strand	344-346	3	1
α-helix	353-367	15
α-helix	368-373	6
β-strand	375-377	3	1
α-helix	380-383	4
β-strand	385	1	6
α-helix	387-389	3
α-helix	390-403	14
β-strand	406-407	2	7
α-helix	408-409	2
β-strand	410	1	8
β-strand	426	1	8
β-strand	430-431	2	7
β-strand	439-445	7	1
α-helix	447-449	3
β-strand	450-457	8	1

Chain B: 22 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	44-53	10	9
β-strand	56-57	2	9
α-helix	59-68	10
β-strand	73-75	3	10
α-helix	79-81	3
β-strand	88-90	3	10
β-strand	94	1	11
β-strand	101	1	11
α-helix	103-106	4
α-helix	109-114	6
α-helix	117-133	17
α-helix	140-144	5
β-strand	146-152	7	9
α-helix	157-170	14
α-helix	172-174	3
α-helix	179-183	5
α-helix	187-196	10
β-strand	202	1	9
α-helix	208-210	3
α-helix	211-225	15
β-strand	230-237	8	9
α-helix	242-250	9
β-strand	254	1	12
β-strand	274	1	12
β-strand	276	1	13
β-strand	277	1	10
β-strand	279-287	9	9
α-helix	288-293	6
β-strand	300-309	10	9
α-helix	322-335	14
α-helix	339-341	3
β-strand	344-346	3	9
α-helix	353-367	15
α-helix	368-371	4
β-strand	375-377	3	9
α-helix	380-383	4
β-strand	385	1	13
α-helix	387-389	3
α-helix	390-404	15
β-strand	406-407	2	14
β-strand	410	1	15
β-strand	423	1	9
β-strand	426	1	15
β-strand	430-431	2	14
β-strand	439-445	7	9
α-helix	447-449	3
β-strand	450-457	8	9

Chain C: 5 helices, 0 β-strands

Element	Residues	Length
α-helix	8-21	14
α-helix	36-39	4
α-helix	44-58	15
α-helix	64-69	6
α-helix	73-81	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
3-oxoacyl-[acyl-carrier-protein] synthase, mitochondrial	A, B	protein	425	Homo sapiens	Q9NWU1 (AlphaFold model)
Acyl carrier protein, mitochondrial	C	protein	88	Homo sapiens	O14561 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>9N50_1 3-oxoacyl-[acyl-carrier-protein] synthase, mitochondrial (chains A, B)
GHMSRLHRRVVITGIGLVTPLGVGTHLVWDRLIGGESGIVSLVGEEYKSIPCSVAAYVPR
GSDEGQFNEQNFVSKSDIKSMSSPTIMAIGAAELAMKDSGWHPQSEADQVATGVAIGMGM
IPLEVVSETALNFQTKGYNKVSPFFVPKILVNMAAGQVSIRYKLKGPNHAVSTACTTGAH
AVGDSFRFIAHGDADVMVAGGTDSCISPLSLAGFSRARALSTNSDPKLACRPFHPKRDGF
VMGEGAAVLVLEEYEHAVQRRARIYAEVLGYGLSGDAGHITAPDPEGEGALRCMAAALKD
AGVQPEEISYINAHATSTPLGDAAENKAIKHLFKDHAYALAVSSTKGATGHLLGAAGAVE
AAFTTLACYYQKLPPTLNLDCSEPEFDLNYVPLKAQEWKTEKRFIGLTNSFGFGGTNATL
CIAGL

Sequence of entity 2 (C), FASTA

>9N50_2 Acyl carrier protein, mitochondrial (chains C)
SDMPPLTLEGIQDRVLYVLKLYDKIDPEKLSVNSHFMKDLGLDSLDQVEIIMAMEDEFGF
EIPDIDAEKLMCPQEIVDYIADKKDVYE

Ligands and cofactors

ID	Name	Formula	Copies
A1BMZ	N~3~-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-N-(2-octanamidoethy…	C19 H38 N3 O8 P	1

Primary citation

Role of Human Mitochondrial Ketosynthase in Long-Chain Fatty Acid Biosynthesis. Suo, Y., Jiang, Z., Heberlig, G.W. et al. J Am Chem Soc (2025) 147:33248-33255. DOI 10.1021/jacs.5c10318 · PubMed

Other PDB entries of the same protein (UniProt Q9NWU1 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2IWZ 1.65 Å, Human mitochondrial beta-ketoacyl ACP synthase complexed with hexanoic acid
2C9H 1.8 Å, Structure of mitochondrial beta-ketoacyl synthase
2IWY 2.06 Å, Human mitochondrial beta-ketoacyl ACP synthase
9N51 2.31 Å, Crosslinked Crystal Structure of Human Mitochondrial Ketosynthase, OXSM, and…

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