4FYT: Human aminopeptidase N

Human aminopeptidase N (CD13) in complex with amastatin. Determined by X-ray diffraction at 1.85 Å resolution. Released 5 Sept 2012.

Method: X-ray diffraction
Resolution: 1.85 Å
Organisms: Homo sapiens, Streptomyces sp. ME98-M3
Chains: 2
Atoms: 8,238
Mol. weight: 107.32 kDa
Ligands: ZN, NAG
Released: 5 Sept 2012

Explore 4FYT in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4FYT contains 51 α-helices and 40 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: 51 helices, 39 β-strands

Element	Residues	Length	Sheet
α-helix	70-72	3
α-helix	76-77	2
β-strand	80-91	12	1
β-strand	102-113	12	1
β-strand	119-123	5	2
β-strand	128-129	2	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	170-171	2
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	427-429	3
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	8
α-helix	514-527	14
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	790-792	3
α-helix	793-803	11
α-helix	806-817	12
α-helix	822-832	11
α-helix	838-848	11
α-helix	856-858	3
α-helix	859-868	10
α-helix	872-882	11
α-helix	884-890	7
α-helix	898-906	9
α-helix	912-924	13
α-helix	931-933	3
α-helix	934-965	32

Chain B: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	2	1	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Aminopeptidase N	A	protein	903	Homo sapiens	P15144 (AlphaFold model)
Amastatin	B	protein	4	Streptomyces sp. ME98-M3

Sequence of entity 1 (A), FASTA

>4FYT_1 Aminopeptidase N (chains A)
PDQSKAWNRYRLPNTLKPDSYRVTLRPYLTPNDRGLYVFKGSSTVRFTCKEATDVIIIHS
KKLNYTLSQGHRVVLRGVGGSQPPDIDKTELVEPTEYLVVHLKGSLVKDSQYEMDSEFEG
ELADDLAGFYRSEYMEGNVRKVVATTQMQAADARKSFPCFDEPAMKAEFNITLIHPKDLT
ALSNMLPKGPSTPLPEDPNWNVTEFHTTPKMSTYLLAFIVSEFDYVEKQASNGVLIRIWA
RPSAIAAGHGDYALNVTGPILNFFAGHYDTPYPLPKSDQIGLPDFNAGAMENWGLVTYRE
NSLLFDPLSSSSSNKERVVTVIAHELAHQWFGNLVTIEWWNDLWLNEGFASYVEYLGADY
AEPTWNLKDLMVLNDVYRVMAVDALASSHPLSTPASEINTPAQISELFDAISYSKGASVL
RMLSSFLSEDVFKQGLASYLHTFAYQNTIYLNLWDHLQEAVNNRSIQLPTTVRDIMNRWT
LQMGFPVITVDTSTGTLSQEHFLLDPDSNVTRPSEFNYVWIVPITSIRDGRQQQDYWLID
VRAQNDLFSTSGNEWVLLNLNVTGYYRVNYDEENWRKIQTQLQRDHSAIPVINRAQIIND
AFNLASAHKVPVTLALNNTLFLIEERQYMPWEAALSSLSYFKLMFDRSEVYGPMKNYLKK
QVTPLFIHFRNNTNNWREIPENLMDQYSEVNAISTACSNGVPECEEMVSGLFKQWMENPN
NNPIHPNLRSTVYCNAIAQGGEEEWDFAWEQFRNATLVNEADKLRAALACSKELWILNRY
LSYTLNPDLIRKQDATSTIISITNNVIGQGLVWDFVQSNWKKLFNDYGGGSFSFSNLIQA
VTRRFSTEYELQQLEQFKKDNEETGFGSGTRALEQALEKTKANIKWVKENKEVVLQWFTE
NSK

Sequence of entity 2 (B), FASTA

>4FYT_2 AMASTATIN (chains B)
XVVD

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	1
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	5

Water and common crystallization additives (SO4) are not listed.

Primary citation

The X-ray Crystal Structure of Human Aminopeptidase N Reveals a Novel Dimer and the Basis for Peptide Processing. Wong, A.H., Zhou, D., Rini, J.M. J Biol Chem (2012) 287:36804-36813. DOI 10.1074/jbc.M112.398842 · 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…
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…
9CAO 3.14 Å, Aminopeptidase N open state

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