5MRI: Vps10p domain of human sortilin/NTS3

Crystal structure of the Vps10p domain of human sortilin/NTS3 in complex with Triazolone 18. Determined by X-ray diffraction at 2.0 Å resolution. Released 17 May 2017.

Method: X-ray diffraction
Resolution: 2.0 Å
Organism: Homo sapiens
Chains: 1
Atoms: 5,686
Mol. weight: 79.24 kDa
Ligands: Q9Y, NAG
Released: 17 May 2017

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

Secondary structure: helices and β-sheets

5MRI contains 20 α-helices and 63 β-strands across 1 chain. 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: 20 helices, 63 β-strands

Element	Residues	Length	Sheet
α-helix	59-64	6
β-strand	67-71	5	1
β-strand	79-83	5	2
β-strand	91-98	8	2
α-helix	102-104	3
β-strand	107-114	8	2
β-strand	122-123	2	2
α-helix	125-128	4
β-strand	131	1	2
β-strand	133	1	3
β-strand	140-141	2	3
α-helix	142	1
β-strand	149-153	5	3
β-strand	163-167	5	3
β-strand	175-178	4	3
β-strand	183	1	4
β-strand	188-189	2	5
β-strand	197-200	4	5
β-strand	201	1	4
β-strand	206-209	4	5
β-strand	217-220	4	5
β-strand	223-228	6	6
β-strand	234-238	5	6
β-strand	251-256	6	6
β-strand	264-276	13	6
β-strand	279-285	7	6
β-strand	292-297	6	6
β-strand	305-306	2	6
β-strand	312	1	6
β-strand	318-323	6	7
β-strand	328-333	6	7
α-helix	334	1
β-strand	340-346	7	7
β-strand	353-361	9	7
β-strand	362	1	8
β-strand	369	1	8
β-strand	372-373	2	7
β-strand	381-386	6	7
β-strand	392-397	6	7
β-strand	405-406	2	7
β-strand	407-408	2	9
α-helix	409-410	2
α-helix	413-415	3
β-strand	426-429	4	9
α-helix	432-436	5
β-strand	446	1	9
β-strand	455-462	8	9
α-helix	469-470	2
β-strand	471-475	5	9
β-strand	483-486	4	9
β-strand	490-495	6	10
α-helix	496-498	3
β-strand	500-505	6	10
β-strand	511	1	1
β-strand	513-517	5	10
β-strand	525-528	4	10
β-strand	534-540	7	1
β-strand	549-556	8	1
α-helix	558-560	3
β-strand	564-570	7	1
β-strand	578	1	11
α-helix	579	1
α-helix	581-583	3
β-strand	584-588	5	12
β-strand	602	1	12
β-strand	605-612	8	12
β-strand	619	1	11
β-strand	627-632	6	12
α-helix	633-634	2
β-strand	635	1	13
α-helix	637-639	3
β-strand	640-642	3	14
β-strand	646-647	2	15
β-strand	656-657	2	15
α-helix	663-671	9
α-helix	674-677	4
β-strand	678-679	2	16
β-strand	682-684	3	14
α-helix	685	1
β-strand	693	1	13
β-strand	701-702	2	16
α-helix	704-708	5
α-helix	712-713	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Sortilin	A	protein	696	Homo sapiens	Q99523 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5MRI_1 Sortilin (chains A)
SAPGEDEECGRVRDFVAKLANNTHQHVFDDLRGSVSLSWVGDSTGVILVLTTFHVPLVIM
TFGQSKLYRSEDYGKNFKDITDLINNTFIRTEFGMAIGPENSGKVVLTAEVSGGSRGGRI
FRSSDFAKNFVQTDLPFHPLTQMMYSPQNSDYLLALSTENGLWVSKNFGGKWEEIHKAVC
LAKWGSDNTIFFTTYANGSCKADLGALELWRTSDLGKSFKTIGVKIYSFGLGGRFLFASV
MADKDTTRRIHVSTDQGDTWSMAQLPSVGQEQFYSILAANDDMVFMHVDEPGDTGFGTIF
TSDDRGIVYSKSLDRHLYTTTGGETDFTNVTSLRGVYITSVLSEDNSIQTMITFDQGGRW
THLRKPENSECDATAKNKNECSLHIHASYSISQKLNVPMAPLSEPNAVGIVIAHGSVGDA
ISVMVPDVYISDDGGYSWTKMLEGPHYYTILDSGGIIVAIEHSSRPINVIKFSTDEGQCW
QTYTFTRDPIYFTGLASEPGARSMNISIWGFTESFLTSQWVSYTIDFKDILERNCEEKDY
TIWLAHSTDPEDYEDGCILGYKEQFLRLRKSSMCQNGRDYVVTKQPSICLCSLEDFLCDF
GYYRPENDSKCVEQPELKGHDLEFCLYGREEHLTTNGYRKIPGDKCQGGVNPVREVKDLK
KKCTSNFLSPEKQNSKSNSGSAMIEGRGVGHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
Q9Y	~{N}-methyl-3-(3-methylbutyl)-5-oxidanyl-1,2,3-triazole-4-carboxamide	C9 H16 N4 O2	1
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	1

Primary citation

The identification of novel acid isostere based inhibitors of the VPS10P family sorting receptor Sortilin. Andersen, J.L., Lindberg, S., Langgard, M. et al. Bioorg Med Chem Lett (2017) 27:2629-2633. DOI 10.1016/j.bmcl.2017.02.028 · PubMed

Other PDB entries of the same protein (UniProt Q99523 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3F6K 2.0 Å, Crystal structure of the Vps10p domain of human sortilin/NTS3 in complex with neurotensin
3G2V 2.1 Å, VHS Domain of human GGA1 complexed with Sotilin C-terminal Phosphopeptide
3G2U 2.3 Å, VHS Domain of human GGA1 complexed with Sotilin C-terminal Peptide
5MRH 2.5 Å, Crystal structure of the Vps10p domain of human sortilin/NTS3 in complex with Triazolone 1
4PO7 2.66 Å, Structure of the Sortilin:neurotensin complex at excess neurotensin concentration
4MSL 2.7 Å, Crystal structure of the Vps10p domain of human sortilin/NTS3 in complex with AF40431
4N7E 2.7 Å, Crystal structure of the Vps10p domain of human sortilin/NTS3 in complex with AF38469
6X3L 2.7 Å, Sortilin-Progranulin Interaction With Compound 2
9R18 2.8 Å, Structure of Sortilin ECD in complex with TNFa-targeting SORTAC
8T8R 2.87 Å, Sortilin-PGRN peptide complex
6X48 2.9 Å, Sortilin-Progranulin Interaction With Compound 17
6X4H 2.9 Å, Sortilin-Progranulin Interaction With Compound 24

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