3F6K: Vps10p domain of human sortilin/NTS3

Crystal structure of the Vps10p domain of human sortilin/NTS3 in complex with neurotensin. Determined by X-ray diffraction at 2.0 Å resolution. Released 30 Dec 2008.

Method: X-ray diffraction
Resolution: 2.0 Å
Organism: Homo sapiens
Chains: 2
Atoms: 5,600
Mol. weight: 79.7 kDa
Released: 30 Dec 2008

Explore 3F6K in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3F6K contains 21 α-helices and 68 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: 21 helices, 67 β-strands

Element	Residues	Length	Sheet
α-helix	59-64	6
β-strand	67-72	6	1
β-strand	78-83	6	2
β-strand	91-97	7	2
β-strand	108-114	7	2
β-strand	122-123	2	2
α-helix	125-128	4
β-strand	133	1	3
α-helix	135-137	3
β-strand	139-141	3	3
α-helix	142	1
β-strand	149-153	5	3
α-helix	154-156	3
β-strand	163-167	5	3
β-strand	175-178	4	3
β-strand	183	1	4
β-strand	188-190	3	5
β-strand	193-200	8	5
β-strand	201	1	4
β-strand	206-209	4	5
β-strand	216-220	5	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
α-helix	286	1
β-strand	292-297	6	6
β-strand	305-306	2	6
β-strand	308	1	7
β-strand	312	1	6
β-strand	318-323	6	8
β-strand	328-333	6	8
α-helix	334	1
β-strand	340-346	7	8
β-strand	352	1	7
β-strand	353-361	9	8
β-strand	362	1	9
β-strand	369	1	9
β-strand	372-373	2	8
β-strand	381-386	6	8
β-strand	392-397	6	8
β-strand	405-406	2	8
β-strand	407-408	2	10
α-helix	409-410	2
β-strand	421	1	11
β-strand	424	1	11
β-strand	426-429	4	10
α-helix	432-436	5
β-strand	446	1	10
β-strand	455-462	8	10
α-helix	469-470	2
β-strand	471-475	5	10
β-strand	483-486	4	10
β-strand	490-495	6	12
α-helix	496-498	3
β-strand	500-505	6	12
β-strand	511	1	13
β-strand	513-517	5	12
β-strand	525-528	4	12
β-strand	534	1	13
β-strand	535-540	6	1
β-strand	549-557	9	1
β-strand	562-570	9	1
α-helix	571-573	3
β-strand	578	1	14
α-helix	581-583	3
β-strand	584-588	5	15
β-strand	602	1	15
β-strand	605-612	8	15
β-strand	619	1	14
β-strand	628-632	5	15
α-helix	633-634	2
β-strand	635	1	16
α-helix	637-639	3
β-strand	640-642	3	17
β-strand	646-647	2	18
β-strand	656-657	2	18
α-helix	663-671	9
α-helix	674-677	4
β-strand	678-679	2	19
β-strand	682-684	3	17
α-helix	685	1
β-strand	693	1	16
β-strand	701-702	2	19
α-helix	704-707	4
α-helix	708-710	3
α-helix	712-715	4

Chain N: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	11-12	2	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Sortilin	A	protein	685	Homo sapiens	Q99523 (AlphaFold model)
Neurotensin	N	protein	13		P30990 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>3F6K_1 Sortilin (chains A)
SAPGEDEECGRVRDFVAKLANNTHQHVFDDLRGSVSLSWVGDSTGVILVLTTFHVPLVIM
TFGQSKLYRSEDYGKNFKDITDLINNTFIRTEFGMAIGPENSGKVVLTAEVSGGSRGGRI
FRSSDFAKNFVQTDLPFHPLTQMMYSPQNSDYLLALSTENGLWVSKNFGGKWEEIHKAVC
LAKWGSDNTIFFTTYANGSCKADLGALELWRTSDLGKSFKTIGVKIYSFGLGGRFLFASV
MADKDTTRRIHVSTDQGDTWSMAQLPSVGQEQFYSILAANDDMVFMHVDEPGDTGFGTIF
TSDDRGIVYSKSLDRHLYTTTGGETDFTNVTSLRGVYITSVLSEDNSIQTMITFDQGGRW
THLRKPENSECDATAKNKNECSLHIHASYSISQKLNVPMAPLSEPNAVGIVIAHGSVGDA
ISVMVPDVYISDDGGYSWTKMLEGPHYYTILDSGGIIVAIEHSSRPINVIKFSTDEGQCW
QTYTFTRDPIYFTGLASEPGARSMNISIWGFTESFLTSQWVSYTIDFKDILERNCEEKDY
TIWLAHSTDPEDYEDGCILGYKEQFLRLRKSSMCQNGRDYVVTKQPSICLCSLEDFLCDF
GYYRPENDSKCVEQPELKGHDLEFCLYGREEHLTTNGYRKIPGDKCQGGVNPVREVKDLK
KKCTSNFLSPEKQNSKSNSHHHHHH

Sequence of entity 2 (N), FASTA

>3F6K_2 Neurotensin (chains N)
QLYENKPRRPYIL

Primary citation

Ligands bind to Sortilin in the tunnel of a ten-bladed beta-propeller domain. Quistgaard, E.M., Madsen, P., Groftehauge, M.K. et al. Nat Struct Mol Biol (2009) 16:96-98. DOI 10.1038/nsmb.1543 · PubMed

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

5MRI 2.0 Å, Crystal structure of the Vps10p domain of human sortilin/NTS3 in complex with Triazolone…
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

Browse structure collections

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