5E3C: Human DPP3

Structure of human DPP3 in complex with hemorphin like opioid peptide IVYPW. Determined by X-ray diffraction at 2.77 Å resolution. Released 13 Apr 2016.

Method: X-ray diffraction
Resolution: 2.77 Å
Organism: Homo sapiens
Chains: 2
Atoms: 5,835
Mol. weight: 82.38 kDa
Ligands: ZN, MG
Released: 13 Apr 2016

Explore 5E3C in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5E3C contains 37 α-helices and 33 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: 37 helices, 32 β-strands

Element	Residues	Length	Sheet
β-strand	7	1	1
β-strand	14-16	3	2
α-helix	20-25	6
α-helix	28-45	18
α-helix	47-50	4
α-helix	56-69	14
α-helix	72-79	8
α-helix	86-102	17
β-strand	106	1	3
β-strand	112	1	4
β-strand	113	1	3
β-strand	115	1	1
α-helix	120-127	8
α-helix	131-135	5
α-helix	137-152	16
β-strand	160	1	4
β-strand	161	1	5
β-strand	168	1	5
β-strand	172	1	6
α-helix	178-190	13
β-strand	198-204	7	6
β-strand	210-217	8	6
β-strand	236-239	4	6
β-strand	242-250	9	6
α-helix	252-266	15
α-helix	272-287	16
α-helix	290-302	13
β-strand	308-314	7	7
α-helix	326-327	2
β-strand	328-335	8	7
α-helix	337-348	12
α-helix	350-354	5
α-helix	361-363	3
β-strand	372-382	11	7
β-strand	389-392	4	7
α-helix	396-401	6
β-strand	405-409	5	7
α-helix	410-416	7
α-helix	429-448	20
α-helix	449-455	7
β-strand	462	1	8
β-strand	463	1	9
β-strand	469	1	9
β-strand	477	1	10
β-strand	484	1	10
β-strand	489	1	8
α-helix	495-498	4
α-helix	500-502	3
α-helix	503-517	15
α-helix	522-527	6
α-helix	533-552	20
α-helix	553-556	4
β-strand	557-558	2	11
β-strand	563-564	2	11
α-helix	567-582	16
β-strand	587-593	7	12
β-strand	599-605	7	12
α-helix	609	1
α-helix	610-614	5
α-helix	615-630	16
α-helix	634-644	11
α-helix	655-664	10
α-helix	668-670	3
β-strand	671-673	3	2
β-strand	676-679	4	13
β-strand	684-687	4	13
α-helix	693-701	9
α-helix	708-721	14
α-helix	723-725	3

Chain B: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	3	1	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Dipeptidyl peptidase 3	A	protein	726	Homo sapiens	Q9NY33 (AlphaFold model)
Ivypw	B	protein	5	Homo sapiens

Sequence of entity 1 (A), FASTA

>5E3C_1 Dipeptidyl peptidase 3 (chains A)
MADTQYILPNDIGVSSLDSREAFRLLSPTERLYAYHLSRAAWYGGLAVLLQTSPEAPYIY
ALLSRLFRAQDPDQLRQHALAEGLTEEEYQAFLVYAAGVYSNMGNYKSFGDTKFVPNLPK
EKLERVILGSEAAQQHPEEVRGLWQTCGELMFSLEPRLRHLGLGKEGITTYFSGNCTMED
AKLAQDFLDSQNLSAYNTRLFKEVDGCGKPYYEVRLASVLGSEPSLDSEVTSKLKSYEFR
GSPFQVTRGDYAPILQKVVEQLEKAKAYAANSHQGQMLAQYIESFTQGSIEAHKRGSRFW
IQDKGPIVESYIGFIESYRDPFGSRGEFEGFVAVVNKAMSAKFERLVASAEQLLKELPWP
PTFEKDKFLTPDFTSLDVLTFAGSGIPAGINIPNYDDLRQTEGFKNVSLGNVLAVAYATQ
REKLTFLEEDDKDLYILWKGPSFDVQVGLHALLGHGSGKLFVQDEKGAFNFDQETVINPE
TGEQIQSWYRCGETWDSKFSTIASSYEECRAESVGLYLSLHPQVLEIFGFEGADAEDVIY
VNWLNMVRAGLLALEFYTPEAFNWRQAHMQARFVILRVLLEAGEGLVTITPTTGSDGRPD
ARVRLDRSKIRSVGKPALERFLRRLQVLKSTGDVAGGRALYEGYATVTDAPPESFLTLRD
TVLLRKESRKLIVQPNTRLEGSDVQLLEYEASAAGLIRSFSERFPEDGPELEEILTQLAT
ADARFW

Sequence of entity 2 (B), FASTA

>5E3C_2 IVYPW (chains B)
IVYPW

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	1
MG	Magnesium ion	Mg	2

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

Primary citation

Substrate complexes of human dipeptidyl peptidase III reveal the mechanism of enzyme inhibition. Kumar, P., Reithofer, V., Reisinger, M. et al. Sci Rep (2016) 6:23787-23787. DOI 10.1038/srep23787 · PubMed

Other PDB entries of the same protein (UniProt Q9NY33 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5E33 1.84 Å, Structure of human DPP3 in complex with met-enkephalin
3FVY 1.9 Å, Crystal structure of human Dipeptidyl Peptidase III
5E3A 2.05 Å, Structure of human DPP3 in complex with opioid peptide leu-enkephalin
5EHH 2.38 Å, Structure of human DPP3 in complex with endomorphin-2.
3T6B 2.4 Å, Structure of human DPPIII in complex with the opioid peptide Tynorphin, at 2.4 Angstroms
5E2Q 2.4 Å, Structure of human DPP3 in complex with angiotensin-II
7OUP 2.65 Å, Structure of human DPP3 in complex with a hydroxyethylene transition state peptidomimetic
5EGY 2.74 Å, Structure of ligand free human DPP3 in closed form.
3T6J 2.98 Å, Structure of human DPPIII in complex with the opioid peptide Tynorphin, at 3.0 Angstroms

Browse structure collections

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