5LDS: Porcine aminopeptidase N ectodomain

Structure of the porcine aminopeptidase N ectodomain. Determined by X-ray diffraction at 2.0 Å resolution. Released 5 Apr 2017.

Method: X-ray diffraction
Resolution: 2.0 Å
Organism: Sus scrofa
Chains: 4
Atoms: 34,579
Mol. weight: 440.53 kDa
Ligands: ZN, NAG
Released: 5 Apr 2017

Explore 5LDS in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5LDS contains 199 α-helices and 148 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: 51 helices, 37 β-strands

Element	Residues	Length	Sheet
α-helix	66-68	3
α-helix	72-73	2
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	143-144	2
β-strand	145-151	7	2
β-strand	156-161	6	2
α-helix	164-166	3
β-strand	170-180	11	1
β-strand	187-195	9	3
β-strand	198-206	9	3
α-helix	212-214	3
β-strand	218	1	2
β-strand	226	1	4
β-strand	227-235	9	1
β-strand	239-242	4	3
α-helix	245	1
β-strand	246	1	5
β-strand	251-253	3	1
β-strand	256-263	8	1
β-strand	264	1	5
α-helix	265-268	4
β-strand	270	1	4
α-helix	272-274	3
β-strand	277-280	4	3
β-strand	283-288	6	6
β-strand	294-299	6	6
α-helix	301-305	5
α-helix	310-326	17
β-strand	335-341	7	6
β-strand	348-349	2	6
β-strand	354-358	5	6
α-helix	359-361	3
α-helix	371-386	16
β-strand	390	1	7
β-strand	394-396	3	7
α-helix	399-401	3
α-helix	403-420	18
α-helix	422-424	3
α-helix	426-429	4
α-helix	430	1
α-helix	431-435	5
α-helix	436-442	7
α-helix	454-456	3
α-helix	460-465	6
α-helix	469	1
α-helix	470-474	5
α-helix	475-486	12
α-helix	488-502	15
β-strand	505-507	3	7
α-helix	509-521	13
α-helix	532-540	9
β-strand	546-551	6	8
β-strand	556-561	6	8
β-strand	582-584	3	9
β-strand	586-588	3	10
β-strand	591-592	2	10
β-strand	596-598	3	9
β-strand	603-605	3	8
α-helix	607-609	3
β-strand	617-619	3	10
α-helix	621-623	3
β-strand	628-631	4	8
α-helix	633-646	14
α-helix	647-649	3
α-helix	652-667	16
α-helix	673-678	6
α-helix	681-685	5
α-helix	689-706	18
α-helix	712-733	22
α-helix	744-759	16
α-helix	763-777	15
α-helix	787-789	3
α-helix	790-800	11
α-helix	803-815	13
α-helix	819-829	11
α-helix	835-844	10
α-helix	853-855	3
α-helix	856-865	10
α-helix	869-879	11
α-helix	881-888	8
α-helix	894-903	10
α-helix	909-921	13
α-helix	928-930	3
α-helix	931-962	32

Chain B: 49 helices, 37 β-strands

Element	Residues	Length	Sheet
α-helix	66-68	3
α-helix	72-73	2
β-strand	76-87	12	11
β-strand	98-109	12	11
β-strand	113-119	7	12
β-strand	124-125	2	11
β-strand	132-136	5	11
α-helix	143-144	2
β-strand	145-151	7	12
β-strand	156-165	10	12
α-helix	166	1
β-strand	170-180	11	11
β-strand	187-195	9	13
β-strand	198-206	9	13
α-helix	212-214	3
β-strand	218	1	12
β-strand	226	1	14
β-strand	227-235	9	11
β-strand	239-242	4	13
β-strand	246	1	15
β-strand	251-252	2	11
β-strand	259-263	5	11
β-strand	264	1	15
α-helix	265-268	4
β-strand	270	1	14
α-helix	272-274	3
β-strand	277-280	4	13
β-strand	283-288	6	16
β-strand	294-299	6	16
α-helix	301-305	5
α-helix	310-326	17
β-strand	335-341	7	16
β-strand	348-349	2	16
β-strand	354-358	5	16
α-helix	359-361	3
α-helix	371-386	16
β-strand	390	1	17
β-strand	394-396	3	17
α-helix	399-401	3
α-helix	403-420	18
α-helix	422-424	3
α-helix	426-429	4
α-helix	430	1
α-helix	431-435	5
α-helix	436-442	7
α-helix	454-456	3
α-helix	460-465	6
α-helix	469	1
α-helix	470-474	5
α-helix	475-486	12
α-helix	488-502	15
β-strand	505-507	3	17
α-helix	509-521	13
α-helix	532-540	9
β-strand	546-551	6	18
β-strand	556-561	6	18
β-strand	582-584	3	19
β-strand	586-588	3	20
β-strand	591-592	2	20
β-strand	596-598	3	19
β-strand	603-605	3	18
α-helix	607-609	3
β-strand	617-619	3	20
α-helix	621-623	3
β-strand	628-631	4	18
α-helix	633-646	14
α-helix	647-649	3
α-helix	652-667	16
α-helix	673-678	6
α-helix	681-685	5
α-helix	689-706	18
α-helix	712-733	22
α-helix	744-759	16
α-helix	763-778	16
α-helix	787-800	14
α-helix	803-814	12
α-helix	819-829	11
α-helix	835-844	10
α-helix	853-855	3
α-helix	856-865	10
α-helix	869-879	11
α-helix	881-888	8
α-helix	894-903	10
α-helix	909-921	13
α-helix	928-930	3
α-helix	931-962	32

Chain C: 49 helices, 37 β-strands

Element	Residues	Length	Sheet
α-helix	66-68	3
α-helix	72-73	2
β-strand	76-87	12	21
β-strand	98-109	12	21
β-strand	115-119	5	22
β-strand	124-125	2	21
β-strand	132-136	5	21
α-helix	143-144	2
β-strand	145-151	7	22
β-strand	156-161	6	22
α-helix	164-166	3
β-strand	170-180	11	21
β-strand	187-195	9	23
β-strand	198-206	9	23
α-helix	212-214	3
β-strand	218	1	22
β-strand	226	1	24
β-strand	227-235	9	21
β-strand	239-242	4	23
α-helix	245	1
β-strand	246	1	25
β-strand	251-253	3	21
β-strand	256-263	8	21
β-strand	264	1	25
α-helix	265-268	4
β-strand	270	1	24
α-helix	272-274	3
β-strand	277-280	4	23
β-strand	283-288	6	26
β-strand	294-299	6	26
α-helix	301-305	5
α-helix	310-326	17
β-strand	335-341	7	26
β-strand	348-349	2	26
β-strand	354-358	5	26
α-helix	359-362	4
α-helix	371-389	19
β-strand	390	1	27
β-strand	394-396	3	27
α-helix	399-401	3
α-helix	403-420	18
α-helix	426-429	4
α-helix	430	1
α-helix	431-435	5
α-helix	436-442	7
α-helix	454-456	3
α-helix	460-465	6
α-helix	469	1
α-helix	470-474	5
α-helix	475-486	12
α-helix	488-502	15
β-strand	505-507	3	27
α-helix	509-521	13
α-helix	532-540	9
β-strand	546-551	6	28
β-strand	556-561	6	28
β-strand	582-584	3	29
β-strand	586-588	3	30
β-strand	591-592	2	30
β-strand	596-598	3	29
β-strand	603-605	3	28
α-helix	607-609	3
β-strand	617-619	3	30
α-helix	621-623	3
β-strand	628-631	4	28
α-helix	633-646	14
α-helix	647-649	3
α-helix	652-667	16
α-helix	673-678	6
α-helix	681-685	5
α-helix	689-706	18
α-helix	712-733	22
α-helix	744-759	16
α-helix	763-778	16
α-helix	787-800	14
α-helix	803-814	12
α-helix	819-829	11
α-helix	835-844	10
α-helix	853-855	3
α-helix	856-865	10
α-helix	869-879	11
α-helix	881-888	8
α-helix	894-903	10
α-helix	909-921	13
α-helix	928-930	3
α-helix	931-961	31

Chain D: 50 helices, 37 β-strands

Element	Residues	Length	Sheet
α-helix	66-68	3
α-helix	72-73	2
β-strand	76-88	13	31
β-strand	98-109	12	31
β-strand	115-119	5	32
β-strand	124-125	2	31
β-strand	133-136	4	31
α-helix	140-144	5
β-strand	145-151	7	32
β-strand	156-161	6	32
α-helix	165-166	2
β-strand	169-180	12	31
β-strand	187-195	9	33
β-strand	198-206	9	33
α-helix	212-214	3
β-strand	218	1	32
β-strand	226	1	34
β-strand	227-235	9	31
β-strand	239-242	4	33
β-strand	246	1	35
β-strand	251-253	3	31
β-strand	256-263	8	31
β-strand	264	1	35
α-helix	265-268	4
β-strand	270	1	34
α-helix	272-274	3
β-strand	277-280	4	33
β-strand	283-288	6	36
β-strand	294-299	6	36
α-helix	301-305	5
α-helix	310-326	17
β-strand	335-341	7	36
β-strand	348-349	2	36
β-strand	354-358	5	36
α-helix	359-361	3
α-helix	371-389	19
β-strand	390	1	37
β-strand	394-396	3	37
α-helix	399-401	3
α-helix	403-420	18
α-helix	422-424	3
α-helix	426-429	4
α-helix	430	1
α-helix	431-435	5
α-helix	436-442	7
α-helix	454-456	3
α-helix	460-465	6
α-helix	469	1
α-helix	470-474	5
α-helix	475-486	12
α-helix	488-502	15
β-strand	505-507	3	37
α-helix	509-521	13
α-helix	532-540	9
β-strand	546-551	6	38
β-strand	556-561	6	38
β-strand	582-584	3	39
β-strand	586-588	3	40
β-strand	591-592	2	40
α-helix	593-595	3
β-strand	596-598	3	39
β-strand	603-605	3	38
α-helix	607-609	3
β-strand	617-619	3	40
α-helix	621-623	3
β-strand	628-631	4	38
α-helix	633-646	14
α-helix	647-649	3
α-helix	652-667	16
α-helix	673-678	6
α-helix	681-685	5
α-helix	689-706	18
α-helix	712-733	22
α-helix	744-759	16
α-helix	763-777	15
α-helix	787-789	3
α-helix	790-800	11
α-helix	803-814	12
α-helix	819-829	11
α-helix	835-844	10
α-helix	853-865	13
α-helix	869-879	11
α-helix	881-888	8
α-helix	894-903	10
α-helix	909-921	13
α-helix	928-930	3
α-helix	931-961	31

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Aminopeptidase N	A, B, C, D	protein	945	Sus scrofa	P15145 (AlphaFold model)

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

>5LDS_1 Aminopeptidase N (chains A, B, C, D)
YPYDVPDYAGAQPARSPEKNKNAEHVPQAPTSPTITTTAAITLDQSKPWNRYRLPTTLLP
DSYNVTLRPYLTPNADGLYIFKGKSIVRFICQEPTDVIIIHSKKLNYTTQGHMVVLRGVG
DSQVPEIDRTELVELTEYLVVHLKGSLQPGHMYEMESEFQGELADDLAGFYRSEYMEGNV
KKVLATTQMQSTDARKSFPCFDEPAMKATFNITLIHPNNLTALSNMPPKGSSTPLAEDPN
WSVTEFETTPVMSTYLLAYIVSEFQSVNETAQNGVLIRIWARPNAIAEGHGMYALNVTGP
ILNFFANHYNTSYPLPKSDQIALPDFNAGAMENWGLVTYRENALLFDPQSSSISNKERVV
TVIAHELAHQWFGNLVTLAWWNDLWLNEGFASYVEYLGADHAEPTWNLKDLIVPGDVYRV
MAVDALASSHPLTTPAEEVNTPAQISEMFDSISYSKGASVIRMLSNFLTEDLFKEGLASY
LHAFAYQNTTYLDLWEHLQKAVDAQTSIRLPDTVRAIMDRWTLQMGFPVITVDTKTGNIS
QKHFLLDSESNVTRSSAFDYLWIVPISSIKNGVMQDHYWLRDVSQAQNDLFKTASDDWVL
LNVNVTGYFQVNYDEDNWRMIQHQLQTNLSVIPVINRAQVIYDSFNLATAHMVPVTLALD
NTLFLNGEKEYMPWQAALSSLSYFSLMFDRSEVYGPMKKYLRKQVEPLFQHFETLTKNWT
ERPENLMDQYSEINAISTACSNGLPQCENLAKTLFDQWMSDPENNPIHPNLRSTIYCNAI
AQGGQDQWDFAWGQLQQAQLVNEADKLRSALACSNEVWLLNRYLGYTLNPDLIRKQDATS
TINSIASNVIGQPLAWDFVQSNWKKLFQDYGGGSFSFSNLIQGVTRRFSSEFELQQLEQF
KKNNMDVGFGSGTRALEQALEKTKANIKWVKENKEVVLNWFIEHS

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	4
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	16

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

Primary citation

Allosteric inhibition of aminopeptidase N functions related to tumor growth and virus infection. Santiago, C., Mudgal, G., Reguera, J. et al. Sci Rep (2017) 7:46045-46045. DOI 10.1038/srep46045 · 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
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
6BV3 2.2 Å, Crystal structure of porcine aminopeptidase-N with Leucine

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