4F5C: Aminopeptidase N

Crystal structure of the spike receptor binding domain of a porcine respiratory coronavirus in complex with the pig aminopeptidase N ectodomain. Determined by X-ray diffraction at 3.2 Å resolution. Released 22 Aug 2012.

Method: X-ray diffraction
Resolution: 3.2 Å
Organisms: Sus scrofa, Porcine respiratory coronavirus
Chains: 4
Atoms: 17,067
Mol. weight: 320.35 kDa
Ligands: ZN, NAG
Released: 22 Aug 2012

Explore 4F5C in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4F5C contains 91 α-helices and 103 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: 45 helices, 39 β-strands

Element	Residues	Length	Sheet
β-strand	76-88	13	1
β-strand	98-109	12	1
β-strand	115-119	5	2
β-strand	124-125	2	1
β-strand	133-136	4	1
α-helix	143	1
β-strand	144-145	2	3
β-strand	150-151	2	2
β-strand	156-160	5	2
β-strand	161-162	2	3
β-strand	170-180	11	1
β-strand	187-195	9	4
β-strand	198-206	9	4
β-strand	218	1	2
β-strand	226	1	5
β-strand	227-235	9	1
β-strand	239-242	4	4
β-strand	246	1	6
β-strand	251-252	2	1
β-strand	259-263	5	1
β-strand	264	1	6
α-helix	265-267	3
β-strand	270	1	5
β-strand	277-280	4	4
β-strand	283-288	6	7
β-strand	294-299	6	7
α-helix	301-305	5
α-helix	307-309	3
α-helix	311-314	4
α-helix	316-326	11
β-strand	335-341	7	7
β-strand	348-349	2	7
β-strand	354-358	5	7
α-helix	359-362	4
α-helix	371-386	16
β-strand	390	1	8
β-strand	394-396	3	8
α-helix	399-401	3
α-helix	402-420	19
α-helix	426-429	4
α-helix	430	1
α-helix	431-435	5
α-helix	436-439	4
α-helix	454-456	3
α-helix	460-464	5
α-helix	470-474	5
α-helix	475-485	11
α-helix	488-502	15
β-strand	505-507	3	8
α-helix	510-520	11
α-helix	532-540	9
β-strand	546-551	6	9
β-strand	556-561	6	9
β-strand	582-584	3	10
β-strand	586-588	3	11
β-strand	591-592	2	11
β-strand	596-598	3	10
β-strand	603-605	3	9
α-helix	607-609	3
β-strand	617-619	3	11
α-helix	621-623	3
β-strand	628-631	4	9
α-helix	635-644	10
α-helix	647-649	3
α-helix	652-668	17
α-helix	673-678	6
α-helix	681-685	5
α-helix	689-699	11
α-helix	702-705	4
α-helix	712-733	22
α-helix	744-759	16
α-helix	763-777	15
α-helix	787-797	11
α-helix	803-815	13
α-helix	819-828	10
α-helix	829-831	3
α-helix	835-844	10
α-helix	853-864	12
α-helix	869-879	11
α-helix	881-886	6
α-helix	895-902	8
α-helix	903-905	3
α-helix	909-921	13
α-helix	932-961	30

Chain B: 44 helices, 40 β-strands

Element	Residues	Length	Sheet
β-strand	76-92	17	12
β-strand	96-109	14	12
β-strand	113-119	7	13
β-strand	124-125	2	12
β-strand	133-136	4	12
β-strand	144-145	2	14
β-strand	150-151	2	13
β-strand	156-160	5	13
β-strand	161-162	2	14
β-strand	163-165	3	13
β-strand	170-180	11	12
β-strand	187-195	9	15
β-strand	198-206	9	15
β-strand	218	1	13
β-strand	226	1	16
β-strand	227-235	9	12
β-strand	239-242	4	15
β-strand	246	1	17
β-strand	251-252	2	12
β-strand	259-263	5	12
β-strand	264	1	17
α-helix	265-267	3
β-strand	270	1	16
β-strand	277-280	4	15
β-strand	283-288	6	18
β-strand	294-299	6	18
α-helix	301-305	5
α-helix	307-309	3
α-helix	311-314	4
α-helix	316-326	11
β-strand	335-341	7	18
β-strand	348-349	2	18
β-strand	354-358	5	18
α-helix	359-362	4
α-helix	371-386	16
β-strand	390	1	19
β-strand	394-396	3	19
α-helix	399-401	3
α-helix	402-420	19
α-helix	426-429	4
α-helix	430	1
α-helix	431-435	5
α-helix	436-439	4
α-helix	454-456	3
α-helix	460-464	5
α-helix	470-474	5
α-helix	475-485	11
α-helix	488-502	15
β-strand	505-507	3	19
α-helix	510-520	11
α-helix	532-540	9
β-strand	546-551	6	20
β-strand	556-561	6	20
β-strand	582-584	3	21
β-strand	586-588	3	22
β-strand	591-592	2	22
β-strand	596-598	3	21
β-strand	603-605	3	20
α-helix	607-609	3
β-strand	617-619	3	22
α-helix	621-623	3
β-strand	628-631	4	20
α-helix	635-644	10
α-helix	647-649	3
α-helix	652-668	17
α-helix	673-678	6
α-helix	681-685	5
α-helix	689-699	11
α-helix	702-705	4
α-helix	712-733	22
α-helix	744-759	16
α-helix	763-777	15
α-helix	787-797	11
α-helix	803-815	13
α-helix	819-828	10
α-helix	829-831	3
α-helix	835-844	10
α-helix	853-864	12
α-helix	869-879	11
α-helix	881-886	6
α-helix	895-902	8
α-helix	903-905	3
α-helix	909-921	13
α-helix	932-961	30

Chain E: 1 helix, 12 β-strands

Element	Residues	Length	Sheet
α-helix	284-286	3
β-strand	288-296	9	23
β-strand	298-301	4	24
β-strand	307-309	3	24
β-strand	314-316	3	23
β-strand	326-328	3	23
β-strand	333-340	8	23
β-strand	343-344	2	24
β-strand	354	1	24
β-strand	362-366	5	23
β-strand	382-389	8	23
β-strand	397-405	9	23
β-strand	408-427	20	23

Chain F: 1 helix, 12 β-strands

Element	Residues	Length	Sheet
β-strand	288-296	9	25
β-strand	298-301	4	26
β-strand	307-309	3	26
β-strand	314-316	3	25
β-strand	326-328	3	25
β-strand	333-340	8	25
β-strand	343-344	2	26
β-strand	354	1	26
α-helix	355	1
β-strand	362-366	5	25
β-strand	381-389	9	25
β-strand	397-404	8	25
β-strand	409-427	19	25

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Aminopeptidase N	A, B	protein	959	Sus scrofa	P15145 (AlphaFold model)
PRCV spike protein	E, F	protein	440	Porcine respiratory coronavirus	Q84852

Sequence of entity 1 (A, B), FASTA

>4F5C_1 Aminopeptidase N (chains A, B)
YPYDVPDYAGAQPARSPEKNKNAEHVPQAPTSPTITTTAAITLDQSKPWNRYRLPTTLLP
DSYNVTLRPYLTPNADGLYIFKGKSIVRFICQEPTDVIIIHSKKLNYTTQGHMVVLRGVG
DSQVPEIDRTELVELTEYLVVHLKGSLQPGHMYEMESEFQGELADDLAGFYRSEYMEGNV
KKVLATTQMQSTDARKSFPCFDEPAMKATFNITLIHPNNLTALSNMPPKGSSTPLAEDPN
WSVTEFETTPVMSTYLLAYIVSEFQSVNETAQNGVLIRIWARPNAIAEGHGMYALNVTGP
ILNFFANHYNTSYPLPKSDQIALPDFNAGAMENWGLVTYRENALLFDPQSSSISNKERVV
TVIAHELAHQWFGNLVTLAWWNDLWLNEGFASYVEYLGADHAEPTWNLKDLIVPGDVYRV
MAVDALASSHPLTTPAEEVNTPAQISEMFDSISYSKGASVIRMLSNFLTEDLFKEGLASY
LHAFAYQNTTYLDLWEHLQKAVDAQTSIRLPDTVRAIMDRWTLQMGFPVITVDTKTGNIS
QKHFLLDSESNVTRSSAFDYLWIVPISSIKNGVMQDHYWLRDVSQAQNDLFKTASDDWVL
LNVNVTGYFQVNYDEDNWRMIQHQLQTNLSVIPVINRAQVIYDSFNLATAHMVPVTLALD
NTLFLNGEKEYMPWQAALSSLSYFSLMFDRSEVYGPMKKYLRKQVEPLFQHFETLTKNWT
ERPENLMDQYSEINAISTACSNGLPQCENLAKTLFDQWMSDPENNPIHPNLRSTIYCNAI
AQGGQDQWDFAWGQLQQAQLVNEADKLRSALACSNEVWLLNRYLGYTLNPDLIRKQDATS
TINSIASNVIGQPLAWDFVQSNWKKLFQDYGGGSFSFSNLIQGVTRRFSSEFELQQLEQF
KKNNMDVGFGSGTRALEQALEKTKANIKWVKENKEVVLNWFIEHSLVPRGSDYKDDDDK

Sequence of entity 2 (E, F), FASTA

>4F5C_2 PRCV spike protein (chains E, F)
DKFPTSVVSNCTDQCASYVANVFTTQPGGFIPSDFSFNNWFLLTNSSTLVSGKLVTKQPL
LVNCLWPVPSFEEAASTFCFEGADFDQCNGAVLNNTVDVIRFNLNFTTNVQSGKGATVFS
LNTTGGVTLEISCYNDTVSDSSFSSYGEIPFGVTNGPRYCYVLYNGTALKYLGTLPPSVK
EIAISKWGHFYINGYNFFSTFPIDCISFNLTTGDSDVFWTIAYTSYTEALVQVENTAITN
VTYCNSYVNNIKCSQLTANLNNGFYPVSSSEVGSVNKSVVLLPSFLTHTIVNITIGLGMK
RSGYGQPIASTLSNITLPMQDNNTDVYCVRSDQFSVYVHSTCKSALWDNVFKRNCTDVLD
ATAVIKTGTCPFSFDKLNNYLTFNKFCLSLSPVGANCKFDVAARTRTNDQVVRSLYVIYE
EGDSIVLVPRGSDYKDDDDK

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	20

Primary citation

Structural bases of coronavirus attachment to host aminopeptidase N and its inhibition by neutralizing antibodies. Reguera, J., Santiago, C., Mudgal, G. et al. PLoS Pathog (2012) 8:e1002859-e1002859. DOI 10.1371/journal.ppat.1002859 · PubMed

Other PDB entries of the same protein (UniProt P15145 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4FKE 1.85 Å, Crystal structure of porcine aminopeptidase-N
6BV0 1.86 Å, Crystal structure of porcine aminopeptidase-N with Arginine
4HOM 1.9 Å, Crystal structure of porcine aminopeptidase-N complexed with substance P
4OU3 1.95 Å, Crystal structure of porcine aminopeptidase N complexed with CNGRCG tumor-homing peptide
4NZ8 2.0 Å, Crystal structure of porcine aminopeptidase-N complexed with cleaved poly-alanine
5LDS 2.0 Å, Structure of the porcine aminopeptidase N ectodomain
6BV1 2.0 Å, Crystal structure of porcine aminopeptidase-N with Aspartic acid
6BV4 2.02 Å, Crystal structure of porcine aminopeptidase-N with Methionine
4FKH 2.05 Å, Crystal structure of porcine aminopeptidase-N complexed with alanine
4NAQ 2.1 Å, Crystal structure of porcine aminopeptidase-N complexed with poly-alanine
6BUY 2.1 Å, Crystal structure of porcine aminopeptidase-N with Glycine
6BV2 2.14 Å, Crystal structure of porcine aminopeptidase-N with Isoleucine

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