3T6B: Human DPPIII

Structure of human DPPIII in complex with the opioid peptide Tynorphin, at 2.4 Angstroms. Determined by X-ray diffraction at 2.4 Å resolution. Released 4 Apr 2012.

Method: X-ray diffraction
Resolution: 2.4 Å
Organism: Homo sapiens
Chains: 4
Atoms: 11,875
Mol. weight: 164.54 kDa
Released: 4 Apr 2012

Explore 3T6B in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3T6B contains 78 α-helices and 62 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: 38 helices, 30 β-strands

Element	Residues	Length	Sheet
β-strand	14-16	3	1
α-helix	21-24	4
α-helix	28-45	18
α-helix	47-50	4
α-helix	56-69	14
α-helix	72-81	10
α-helix	86-102	17
β-strand	106	1	2
β-strand	112	1	3
β-strand	113	1	2
α-helix	120-128	9
α-helix	131-135	5
α-helix	137-152	16
α-helix	156-158	3
β-strand	160	1	3
β-strand	161	1	4
β-strand	168	1	4
β-strand	172	1	5
α-helix	178-190	13
β-strand	198-204	7	5
β-strand	210-217	8	5
α-helix	231-233	3
β-strand	236-239	4	5
β-strand	242-250	9	5
α-helix	252-268	17
α-helix	272-287	16
α-helix	290-302	13
β-strand	308-316	9	6
α-helix	325-326	2
β-strand	327-335	9	6
α-helix	340-348	9
α-helix	350-353	4
α-helix	354-356	3
β-strand	373-382	10	6
β-strand	389-392	4	6
α-helix	396-401	6
β-strand	405-409	5	6
α-helix	410-415	6
α-helix	421-423	3
α-helix	429-449	21
α-helix	450-455	6
β-strand	462	1	7
β-strand	463	1	8
β-strand	469	1	8
β-strand	478	1	9
β-strand	483	1	9
β-strand	489	1	7
α-helix	495-518	24
α-helix	522-527	6
α-helix	535-552	18
α-helix	553-556	4
β-strand	557-558	2	10
β-strand	563-564	2	10
α-helix	567-581	15
β-strand	587-593	7	11
β-strand	599-605	7	11
α-helix	607-609	3
α-helix	610-614	5
α-helix	615-630	16
α-helix	634-644	11
α-helix	655-665	11
α-helix	668-670	3
β-strand	671-673	3	1
β-strand	676-679	4	12
β-strand	684-687	4	12
α-helix	693-701	9
α-helix	708-721	14
α-helix	723-725	3

Chain B: 40 helices, 30 β-strands

Element	Residues	Length	Sheet
β-strand	14-16	3	13
α-helix	21-24	4
α-helix	28-45	18
α-helix	47-50	4
α-helix	56-69	14
α-helix	72-81	10
α-helix	86-102	17
β-strand	106	1	14
β-strand	112	1	15
β-strand	113	1	14
α-helix	120-128	9
α-helix	131-135	5
α-helix	137-152	16
α-helix	156-158	3
β-strand	160	1	15
β-strand	161	1	16
β-strand	168	1	16
β-strand	172	1	17
α-helix	178-190	13
β-strand	198-204	7	17
β-strand	210-217	8	17
α-helix	231-233	3
β-strand	236-239	4	17
β-strand	242-250	9	17
α-helix	252-267	16
α-helix	272-287	16
α-helix	290-302	13
β-strand	308-316	9	18
α-helix	325-326	2
β-strand	327-335	9	18
α-helix	337-348	12
α-helix	352-356	5
α-helix	361-363	3
β-strand	373-382	10	18
β-strand	389-392	4	18
α-helix	396-401	6
β-strand	405-409	5	18
α-helix	410-413	4
α-helix	421-423	3
α-helix	429-449	21
α-helix	450-455	6
β-strand	462	1	19
β-strand	463	1	20
β-strand	469	1	20
β-strand	477	1	21
β-strand	484	1	21
β-strand	489	1	19
α-helix	495-499	5
α-helix	500-502	3
α-helix	503-518	16
α-helix	522-527	6
α-helix	535-552	18
α-helix	553-556	4
β-strand	557-558	2	22
β-strand	563-564	2	22
α-helix	567-580	14
β-strand	587-593	7	23
β-strand	599-605	7	23
α-helix	609	1
α-helix	610-614	5
α-helix	615-631	17
α-helix	634-644	11
α-helix	655-664	10
α-helix	668-670	3
β-strand	671-673	3	13
β-strand	676-679	4	24
β-strand	684-687	4	24
α-helix	693-701	9
α-helix	708-721	14
α-helix	723-725	3

Chains C and D: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	2-3	2	6

Molecules and chains

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

Sequence of entity 1 (A, B), FASTA

>3T6B_1 Dipeptidyl peptidase 3 (chains A, B)
MADTQYILPNDIGVSSLDCREAFRLLSPTERLYAYHLSRAAWYGGLAVLLQTSPEAPYIY
ALLSRLFRAQDPDQLRQHALAEGLTEEEYQAFLVYAAGVYSNMGNYKSFGDTKFVPNLPK
EKLERVILGSEAAQQHPEEVRGLWQTCGELMFSLEPRLRHLGLGKEGITTYFSGNCTMED
AKLAQDFLDSQNLSAYNTRLFKEVDGEGKPYYEVRLASVLGSEPSLDSEVTSKLKSYEFR
GSPFQVTRGDYAPILQKVVEQLEKAKAYAANSHQGQMLAQYIESFTQGSIEAHKRGSRFW
IQDKGPIVESYIGFIESYRDPFGSRGEFEGFVAVVNKAMSAKFERLVASAEQLLKELPWP
PTFEKDKFLTPDFTSLDVLTFAGSGIPAGINIPNYDDLRQTEGFKNVSLGNVLAVAYATQ
REKLTFLEEDDKDLYILWKGPSFDVQVGLHALLGHGSGKLFVQDEKGAFNFDQETVINPE
TGEQIQSWYRSGETWDSKFSTIASSYEECRAESVGLYLCLHPQVLEIFGFEGADAEDVIY
VNWLNMVRAGLLALEFYTPEAFNWRQAHMQARFVILRVLLEAGEGLVTITPTTGSDGRPD
ARVRLDRSKIRSVGKPALERFLRRLQVLKSTGDVAGGRALYEGYATVTDAPPECFLTLRD
TVLLRKESRKLIVQPNTRLEGSDVQLLEYEASAAGLIRSFSERFPEDGPELEEILTQLAT
ADARFW

Sequence of entity 2 (C, D), FASTA

>3T6B_2 Tynorphin (chains C, D)
VVYPW

Primary citation

Entropy-driven binding of opioid peptides induces a large domain motion in human dipeptidyl peptidase III. Bezerra, G.A., Dobrovetsky, E., Viertlmayr, R. et al. Proc Natl Acad Sci U S A (2012) 109:6525-6530. DOI 10.1073/pnas.1118005109 · 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.
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.
5E3C 2.77 Å, Structure of human DPP3 in complex with hemorphin like opioid peptide IVYPW
3T6J 2.98 Å, Structure of human DPPIII in complex with the opioid peptide Tynorphin, at 3.0 Angstroms

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