9CAO: Aminopeptidase N open state

Aminopeptidase N open state. Determined by electron microscopy at 3.14 Å resolution. Released 6 Aug 2025.

Method: Electron microscopy
Resolution: 3.14 Å
Organism: Homo sapiens
Chains: 2
Atoms: 14,965
Mol. weight: 226 kDa
Ligands: ZN, NAG
Released: 6 Aug 2025

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

Secondary structure: helices and β-sheets

9CAO contains 91 α-helices and 86 β-strands across 2 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: 47 helices, 45 β-strands

Element	Residues	Length	Sheet
β-strand	80-91	12	13
β-strand	102-113	12	13
β-strand	119-120	2	14
β-strand	123	1	14
β-strand	128-130	3	13
α-helix	131	1
β-strand	132	1	15
β-strand	135	1	15
β-strand	137-141	5	13
α-helix	148-149	2
β-strand	150-156	7	14
β-strand	161-166	6	14
α-helix	169-171	3
β-strand	175-185	11	13
β-strand	192-200	9	16
β-strand	203-211	9	16
α-helix	217-220	4
β-strand	223	1	14
β-strand	231	1	17
β-strand	232-235	4	13
β-strand	236-240	5	18
β-strand	244-247	4	16
α-helix	250	1
β-strand	251	1	19
α-helix	255	1
β-strand	256-257	2	18
α-helix	258	1
β-strand	264-268	5	18
β-strand	269	1	19
α-helix	270-273	4
β-strand	275	1	17
α-helix	277-279	3
β-strand	282-285	4	16
β-strand	288-293	6	20
β-strand	299-304	6	20
α-helix	306-310	5
α-helix	315-331	17
β-strand	340	1	20
β-strand	342-346	5	20
β-strand	353-354	2	20
β-strand	359-363	5	20
α-helix	364-367	4
α-helix	376-394	19
β-strand	395	1	21
β-strand	399-401	3	21
α-helix	404-406	3
α-helix	408-425	18
α-helix	431-435	5
α-helix	436-440	5
α-helix	441-448	8
α-helix	459-461	3
α-helix	465-470	6
α-helix	474	1
α-helix	475-479	5
α-helix	480-491	12
α-helix	493-506	14
β-strand	510-512	3	21
α-helix	514-527	14
α-helix	536-544	9
β-strand	550	1	22
β-strand	551-554	4	23
β-strand	555	1	24
β-strand	560-562	3	24
β-strand	565	1	22
β-strand	586-588	3	25
β-strand	590-592	3	26
β-strand	595-596	2	26
β-strand	600-602	3	25
β-strand	606-608	3	24
β-strand	620-622	3	26
α-helix	624-626	3
β-strand	631-634	4	23
α-helix	636-649	14
α-helix	650-652	3
α-helix	655-670	16
α-helix	676-681	6
α-helix	692-709	18
α-helix	715-736	22
α-helix	747-763	17
α-helix	766-781	16
α-helix	790-803	14
α-helix	806-817	12
α-helix	822-832	11
α-helix	838-849	12
α-helix	856-858	3
α-helix	859-868	10
α-helix	870-882	13
α-helix	884-890	7
α-helix	893-895	3
α-helix	899-905	7
α-helix	912-925	14
α-helix	933-966	34

Chain B: 44 helices, 41 β-strands

Element	Residues	Length	Sheet
β-strand	80-91	12	1
α-helix	97-99	3
β-strand	102-113	12	1
β-strand	117-120	4	2
β-strand	123	1	2
β-strand	130	1	1
β-strand	137-141	5	1
α-helix	148-149	2
β-strand	150-156	7	2
β-strand	161-170	10	2
α-helix	171	1
β-strand	175-185	11	1
β-strand	192-200	9	3
β-strand	203-211	9	3
α-helix	217-220	4
β-strand	223	1	2
β-strand	231	1	4
β-strand	232-240	9	1
β-strand	244-247	4	3
β-strand	251	1	5
β-strand	256-257	2	1
β-strand	264-268	5	1
β-strand	269	1	5
α-helix	270-272	3
β-strand	275	1	4
β-strand	282-285	4	3
β-strand	288-293	6	6
β-strand	299-304	6	6
α-helix	306-310	5
α-helix	312-314	3
α-helix	315-331	17
β-strand	340-346	7	6
β-strand	353-354	2	6
β-strand	359-363	5	6
α-helix	364-367	4
α-helix	376-394	19
β-strand	395	1	7
β-strand	399	1	7
β-strand	401	1	8
α-helix	404-406	3
α-helix	407-425	19
α-helix	431-435	5
α-helix	436-440	5
α-helix	441-447	7
α-helix	465-471	7
α-helix	474	1
α-helix	475-479	5
α-helix	480-491	12
α-helix	493-506	14
β-strand	512	1	8
α-helix	514-528	15
α-helix	536-544	9
β-strand	550	1	9
β-strand	551-555	5	10
β-strand	560-562	3	10
β-strand	565	1	9
α-helix	579-582	4
β-strand	586-588	3	11
β-strand	590-592	3	12
β-strand	595-596	2	12
β-strand	600-602	3	11
β-strand	606-608	3	10
α-helix	610-612	3
β-strand	620-622	3	12
α-helix	624-626	3
β-strand	631-634	4	10
α-helix	636-648	13
α-helix	650-652	3
α-helix	655-670	16
α-helix	676-681	6
α-helix	684-687	4
α-helix	693-709	17
α-helix	715-736	22
α-helix	747-763	17
α-helix	766-781	16
α-helix	790-803	14
α-helix	806-817	12
α-helix	822-832	11
α-helix	838-849	12
α-helix	856-868	13
α-helix	870-890	21
α-helix	898-905	8
α-helix	912-924	13
α-helix	931-933	3
α-helix	937-965	29

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Aminopeptidase N	A, B	protein	967	Homo sapiens	P15144 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>9CAO_1 Aminopeptidase N (chains A, B)
MAKGFYISKSLGILGILLGVAAVCTIIALSVVYSQEKNKNANSSPVASTTPSASATTNPA
SATTLDQSKAWNRYRLPNTLKPDSYRVTLRPYLTPNDRGLYVFKGSSTVRFTCKEATDVI
IIHSKKLNYTLSQGHRVVLRGVGGSQPPDIDKTELVEPTEYLVVHLKGSLVKDSQYEMDS
EFEGELADDLAGFYRSEYMEGNVRKVVATTQMQAADARKSFPCFDEPAMKAEFNITLIHP
KDLTALSNMLPKGPSTPLPEDPNWNVTEFHTTPKMSTYLLAFIVSEFDYVEKQASNGVLI
RIWARPSAIAAGHGDYALNVTGPILNFFAGHYDTPYPLPKSDQIGLPDFNAGAMENWGLV
TYRENSLLFDPLSSSSSNKERVVTVIAHELAHQWFGNLVTIEWWNDLWLNEGFASYVEYL
GADYAEPTWNLKDLMVLNDVYRVMAVDALASSHPLSTPASEINTPAQISELFDAISYSKG
ASVLRMLSSFLSEDVFKQGLASYLHTFAYQNTIYLNLWDHLQEAVNNRSIQLPTTVRDIM
NRWTLQMGFPVITVDTSTGTLSQEHFLLDPDSNVTRPSEFNYVWIVPITSIRDGRQQQDY
WLIDVRAQNDLFSTSGNEWVLLNLNVTGYYRVNYDEENWRKIQTQLQRDHSAIPVINRAQ
IINDAFNLASAHKVPVTLALNNTLFLIEERQYMPWEAALSSLSYFKLMFDRSEVYGPMKN
YLKKQVTPLFIHFRNNTNNWREIPENLMDQYSEVNAISTACSNGVPECEEMVSGLFKQWM
ENPNNNPIHPNLRSTVYCNAIAQGGEEEWDFAWEQFRNATLVNEADKLRAALACSKELWI
LNRYLSYTLNPDLIRKQDATSTIISITNNVIGQGLVWDFVQSNWKKLFNDYGGGSFSFSN
LIQAVTRRFSTEYELQQLEQFKKDNEETGFGSGTRALEQALEKTKANIKWVKENKEVVLQ
WFTENSK

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	5

Primary citation

Aminopeptidase N open state. Lyu, M., Zhang, Z. To be published.

Other PDB entries of the same protein (UniProt P15144 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7AEW 1.2 Å, 14-3-3 sigma bound to bis-phosphorylated aminopeptidase N (APN, CD13) via canonical and…
6XWD 1.6 Å, 14-3-3 sigma bound to canonical mono-phosphorylated aminopeptidase N (APN, CD13) binding…
4FYT 1.85 Å, Human aminopeptidase N (CD13) in complex with amastatin
4FYQ 1.9 Å, Human aminopeptidase N (CD13)
4FYR 1.91 Å, Human aminopeptidase N (CD13) in complex with bestatin
4FYS 2.01 Å, Human aminopeptidase N (CD13) in complex with angiotensin IV
6U7G 2.35 Å, HCoV-229E RBD Class V in complex with human APN
5LHD 2.6 Å, Structure of glycosylated human aminopeptidase N
6U7F 2.75 Å, HCoV-229E RBD Class IV in complex with human APN
9CAM 2.96 Å, Aminopeptidase N close state
6U7E 3.0 Å, HCoV-229E RBD Class III in complex with human APN
7VPQ 3.1 Å, Structures of a deltacoronavirus spike protein bound to porcine and human receptors…

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