6ATK: Aminopeptidase N

Crystal structure of the human coronavirus 229E spike protein receptor binding domain in complex with human aminopeptidase N. Determined by X-ray diffraction at 3.5 Å resolution. Released 6 Dec 2017.

Method: X-ray diffraction
Resolution: 3.5 Å
Organisms: Homo sapiens, Human coronavirus 229E
Chains: 6
Atoms: 23,660
Mol. weight: 363.64 kDa
Ligands: NAG, ZN
Released: 6 Dec 2017

Explore 6ATK in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6ATK contains 145 α-helices and 137 β-strands across 6 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: 48 helices, 39 β-strands

Element	Residues	Length	Sheet
α-helix	70-72	3
α-helix	76-77	2
β-strand	80-92	13	1
β-strand	102-113	12	1
β-strand	119-123	5	2
β-strand	127-129	3	1
α-helix	130-131	2
β-strand	132	1	3
β-strand	135	1	3
β-strand	137-141	5	1
α-helix	147-149	3
β-strand	150-156	7	2
β-strand	161-166	6	2
α-helix	169-171	3
β-strand	175-185	11	1
β-strand	192-200	9	4
β-strand	203-211	9	4
α-helix	217-219	3
β-strand	223	1	2
β-strand	231	1	5
β-strand	232-240	9	1
β-strand	244-247	4	4
β-strand	251	1	6
β-strand	256-258	3	1
β-strand	261-268	8	1
β-strand	269	1	6
α-helix	270-273	4
β-strand	275	1	5
α-helix	277-279	3
β-strand	282-285	4	4
β-strand	288-293	6	7
β-strand	299-304	6	7
α-helix	306-310	5
α-helix	315-331	17
β-strand	340-346	7	7
β-strand	353-354	2	7
β-strand	359-363	5	7
α-helix	364-367	4
α-helix	376-394	19
β-strand	395	1	8
β-strand	399-401	3	8
α-helix	404-406	3
α-helix	408-425	18
α-helix	431-435	5
α-helix	436-441	6
α-helix	442-447	6
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	493-507	15
β-strand	510-512	3	8
α-helix	514-528	15
α-helix	536-544	9
β-strand	550-555	6	9
β-strand	560-565	6	9
β-strand	586-588	3	10
β-strand	590-592	3	11
β-strand	595-596	2	11
β-strand	600-602	3	10
β-strand	606-608	3	9
α-helix	610-612	3
β-strand	620-622	3	11
α-helix	624-626	3
β-strand	631-634	4	9
α-helix	636-649	14
α-helix	650-652	3
α-helix	655-670	16
α-helix	676-681	6
α-helix	684-688	5
α-helix	692-709	18
α-helix	715-736	22
α-helix	747-762	16
α-helix	766-781	16
α-helix	790-803	14
α-helix	806-817	12
α-helix	822-831	10
α-helix	832-834	3
α-helix	838-848	11
α-helix	856-858	3
α-helix	859-868	10
α-helix	872-889	18
α-helix	900-906	7
α-helix	912-925	14
α-helix	931-933	3
α-helix	934-965	32

Chain B: 49 helices, 39 β-strands

Element	Residues	Length	Sheet
α-helix	70-72	3
α-helix	76-77	2
β-strand	80-92	13	12
β-strand	102-113	12	12
β-strand	119-123	5	13
β-strand	127-129	3	12
α-helix	130-131	2
β-strand	132	1	14
β-strand	135	1	14
β-strand	137-141	5	12
α-helix	147-149	3
β-strand	150-156	7	13
β-strand	161-166	6	13
α-helix	169-171	3
β-strand	175-185	11	12
β-strand	192-200	9	15
β-strand	203-211	9	15
α-helix	217-219	3
β-strand	223	1	13
β-strand	231	1	16
β-strand	232-240	9	12
β-strand	244-247	4	15
β-strand	251	1	17
β-strand	256-258	3	12
β-strand	261-268	8	12
β-strand	269	1	17
α-helix	270-273	4
β-strand	275	1	16
α-helix	277-279	3
β-strand	282-285	4	15
β-strand	288-293	6	18
β-strand	299-304	6	18
α-helix	306-310	5
α-helix	315-331	17
β-strand	340-346	7	18
β-strand	353-354	2	18
β-strand	359-363	5	18
α-helix	364-367	4
α-helix	376-394	19
β-strand	395	1	19
β-strand	399-401	3	19
α-helix	404-406	3
α-helix	408-425	18
α-helix	431-434	4
α-helix	435	1
α-helix	436-441	6
α-helix	442-447	6
α-helix	459-461	3
α-helix	465-471	7
α-helix	474	1
α-helix	475-479	5
α-helix	480-491	12
α-helix	493-507	15
β-strand	510-512	3	19
α-helix	514-528	15
α-helix	536-544	9
β-strand	550-555	6	20
β-strand	560-565	6	20
β-strand	586-588	3	21
β-strand	590-592	3	22
β-strand	595-596	2	22
β-strand	600-602	3	21
β-strand	606-608	3	20
α-helix	610-612	3
β-strand	620-622	3	22
α-helix	624-626	3
β-strand	631-634	4	20
α-helix	636-649	14
α-helix	650-652	3
α-helix	655-670	16
α-helix	676-681	6
α-helix	684-688	5
α-helix	692-709	18
α-helix	715-736	22
α-helix	747-762	16
α-helix	766-781	16
α-helix	790-803	14
α-helix	806-817	12
α-helix	822-831	10
α-helix	832-834	3
α-helix	838-848	11
α-helix	856-858	3
α-helix	859-868	10
α-helix	872-888	17
α-helix	900-906	7
α-helix	912-925	14
α-helix	931-933	3
α-helix	934-965	32

Chain C: 48 helices, 39 β-strands

Element	Residues	Length	Sheet
α-helix	70-72	3
α-helix	76-77	2
β-strand	80-92	13	23
β-strand	102-113	12	23
β-strand	119-123	5	24
β-strand	127-129	3	23
α-helix	130-131	2
β-strand	132	1	25
β-strand	135	1	25
β-strand	137-141	5	23
α-helix	147-149	3
β-strand	150-156	7	24
β-strand	161-166	6	24
α-helix	169-171	3
β-strand	175-185	11	23
β-strand	192-200	9	26
β-strand	203-211	9	26
α-helix	217-219	3
β-strand	223	1	24
β-strand	231	1	27
β-strand	232-240	9	23
β-strand	244-247	4	26
β-strand	251	1	28
β-strand	256-258	3	23
β-strand	261-268	8	23
β-strand	269	1	28
α-helix	270-273	4
β-strand	275	1	27
α-helix	277-279	3
β-strand	282-285	4	26
β-strand	288-293	6	29
β-strand	299-304	6	29
α-helix	306-310	5
α-helix	315-331	17
β-strand	340-346	7	29
β-strand	353-354	2	29
β-strand	359-363	5	29
α-helix	364-367	4
α-helix	376-392	17
β-strand	395	1	30
β-strand	399-401	3	30
α-helix	404-406	3
α-helix	408-425	18
α-helix	431-434	4
α-helix	435	1
α-helix	436-441	6
α-helix	442-447	6
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	493-507	15
β-strand	510-512	3	30
α-helix	514-528	15
α-helix	536-544	9
β-strand	550-555	6	31
β-strand	560-565	6	31
β-strand	586-588	3	32
β-strand	590-592	3	33
β-strand	595-596	2	33
β-strand	600-602	3	32
β-strand	606-608	3	31
α-helix	610-612	3
β-strand	620-622	3	33
α-helix	624-626	3
β-strand	631-634	4	31
α-helix	636-649	14
α-helix	650-652	3
α-helix	655-670	16
α-helix	676-681	6
α-helix	684-688	5
α-helix	692-709	18
α-helix	715-736	22
α-helix	747-762	16
α-helix	766-781	16
α-helix	790-803	14
α-helix	806-817	12
α-helix	822-831	10
α-helix	832-834	3
α-helix	838-848	11
α-helix	856-868	13
α-helix	872-888	17
α-helix	900-906	7
α-helix	912-925	14
α-helix	931-933	3
α-helix	934-965	32

Chain D: 0 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	306-309	4	37
β-strand	317	1	7
β-strand	324-327	4	37
β-strand	360-364	5	38
β-strand	400-404	5	38
β-strand	408-411	4	38

Chain E: 0 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	299-307	9	34
β-strand	317	1	18
β-strand	326-329	4	34
β-strand	333	1	35
β-strand	337	1	35
β-strand	339-340	2	36
β-strand	345-352	8	34
β-strand	360-364	5	36
β-strand	381-382	2	34
β-strand	386-388	3	36
β-strand	396-404	9	36
β-strand	408-418	11	36
β-strand	425-427	3	34

Chain F: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	317	1	29

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Aminopeptidase N	A, B, C	protein	905	Homo sapiens	P15144 (AlphaFold model)
Spike glycoprotein	D, E, F	protein	146	Human coronavirus 229E	P15423 (AlphaFold model)

Sequence of entity 1 (A, B, C), FASTA

>6ATK_1 Aminopeptidase N (chains A, B, C)
GRPDQSKAWNRYRLPNTLKPDSYRVTLRPYLTPNDRGLYVFKGSSTVRFTCKEATDVIII
HSKKLNYTLSQGHRVVLRGVGGSQPPDIDKTELVEPTEYLVVHLKGSLVKDSQYEMDSEF
EGELADDLAGFYRSEYMEGNVRKVVATTQMQAADARKSFPCFDEPAMKAEFNITLIHPKD
LTALSNMLPKGPSTPLPEDPNWNVTEFHTTPKMSTYLLAFIVSEFDYVEKQASNGVLIRI
WARPSAIAAGHGDYALNVTGPILNFFAGHYDTPYPLPKSDQIGLPDFNAGAMENWGLVTY
RENSLLFDPLSSSSSNKERVVTVIAHELAHQWFGNLVTIEWWNDLWLNEGFASYVEYLGA
DYAEPTWNLKDLMVLNDVYRVMAVDALASSHPLSTPASEINTPAQISELFDAISYSKGAS
VLRMLSSFLSEDVFKQGLASYLHTFAYQNTIYLNLWDHLQEAVNNRSIQLPTTVRDIMNR
WTLQMGFPVITVDTSTGTLSQEHFLLDPDSNVTRPSEFNYVWIVPITSIRDGRQQQDYWL
IDVRAQNDLFSTSGNEWVLLNLNVTGYYRVNYDEENWRKIQTQLQRDHSAIPVINRAQII
NDAFNLASAHKVPVTLALNNTLFLIEERQYMPWEAALSSLSYFKLMFDRSEVYGPMKNYL
KKQVTPLFIHFRNNTNNWREIPENLMDQYSEVNAISTACSNGVPECEEMVSGLFKQWMEN
PNNNPIHPNLRSTVYCNAIAQGGEEEWDFAWEQFRNATLVNEADKLRAALACSKELWILN
RYLSYTLNPDLIRKQDATSTIISITNNVIGQGLVWDFVQSNWKKLFNDYGGGSFSFSNLI
QAVTRRFSTEYELQQLEQFKKDNEETGFGSGTRALEQALEKTKANIKWVKENKEVVLQWF
TENSK

Sequence of entity 2 (D, E, F), FASTA

>6ATK_2 Spike glycoprotein (chains D, E, F)
GRPLPVYHKHMFIVLYVDFKPQSGGGKCFNCYPAGVNITLANFNETKGPLCVDTSHFTTK
YVAVYANVGRWSASINTGNCPFSFGKVNNFVKFGSVCFSLKDIPGGCAMPIVANWAYSKY
YTIGTLYVSWSDGDGITGVPQPVEGV

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	15
ZN	Zinc ion	Zn	3

Primary citation

Receptor-binding loops in alphacoronavirus adaptation and evolution. Wong, A.H.M., Tomlinson, A.C.A., Zhou, D. et al. Nat Commun (2017) 8:1735-1735. DOI 10.1038/s41467-017-01706-x · PubMed

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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