6X3L: Sortilin-Progranulin Interaction With Compound 2

Sortilin-Progranulin Interaction With Compound 2. Determined by X-ray diffraction at 2.7 Å resolution. Released 12 Aug 2020.

Method: X-ray diffraction
Resolution: 2.7 Å
Organism: Homo sapiens
Chains: 1
Atoms: 5,248
Mol. weight: 86.19 kDa
Ligands: UMJ
Released: 12 Aug 2020

Explore 6X3L in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6X3L contains 17 α-helices and 64 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: 17 helices, 64 β-strands

Element	Residues	Length	Sheet
α-helix	59-64	6
β-strand	67-68	2	1
β-strand	71-72	2	1
β-strand	80-84	5	2
β-strand	90-96	7	2
β-strand	109-114	6	2
β-strand	121	1	2
α-helix	125-128	4
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	205-209	5	5
β-strand	216-222	7	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	292-296	5	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	404-406	3	7
β-strand	407-408	2	9
α-helix	409-410	2
β-strand	426-430	5	9
α-helix	432-436	5
β-strand	446-447	2	9
β-strand	455-462	8	9
α-helix	470-471	2
β-strand	472-475	4	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	11
β-strand	513-517	5	10
β-strand	525-528	4	10
β-strand	534	1	11
β-strand	535-540	6	1
β-strand	549-555	7	1
β-strand	564-570	7	1
β-strand	578	1	12
α-helix	579	1
α-helix	581-583	3
β-strand	584-588	5	13
β-strand	602	1	13
β-strand	605-612	8	13
β-strand	619	1	12
β-strand	627-632	6	13
α-helix	633-634	2
β-strand	635	1	14
α-helix	637-639	3
β-strand	640-642	3	15
β-strand	646-647	2	16
β-strand	656-657	2	16
α-helix	658	1
α-helix	664-671	8
α-helix	674-677	4
β-strand	679	1	17
β-strand	682-684	3	15
α-helix	685	1
β-strand	693	1	14
β-strand	701	1	17

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Sortilin	A	protein	762	Homo sapiens	Q99523 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6X3L_1 Sortilin (chains A)
MERPWGAADGLSRWPHGLGLLLLLQLLPPSTLSQDRLDAPPPPAAPLPRWSGPIGVSWGL
RAAAAGGAFPRGGRWRRSAPGEDEECGRVRDFVAKLANNTHQHVFDDLRGSVSLSWVGDS
TGVILVLTTFHVPLVIMTFGQSKLYRSEDYGKNFKDITDLINNTFIRTEFGMAIGPENSG
KVVLTAEVSGGSRGGRIFRSSDFAKNFVQTDLPFHPLTQMMYSPQNSDYLLALSTENGLW
VSKNFGGKWEEIHKAVCLAKWGSDNTIFFTTYANGSCKADLGALELWRTSDLGKSFKTIG
VKIYSFGLGGRFLFASVMADKDTTRRIHVSTDQGDTWSMAQLPSVGQEQFYSILAANDDM
VFMHVDEPGDTGFGTIFTSDDRGIVYSKSLDRHLYTTTGGETDFTNVTSLRGVYITSVLS
EDNSIQTMITFDQGGRWTHLRKPENSECDATAKNKNECSLHIHASYSISQKLNVPMAPLS
EPNAVGIVIAHGSVGDAISVMVPDVYISDDGGYSWTKMLEGPHYYTILDSGGIIVAIEHS
SRPINVIKFSTDEGQCWQTYTFTRDPIYFTGLASEPGARSMNISIWGFTESFLTSQWVSY
TIDFKDILERNCEEKDYTIWLAHSTDPEDYEDGCILGYKEQFLRLRKSSMCQNGRDYVVT
KQPSICLCSLEDFLCDFGYYRPENDSKCVEQPELKGHDLEFCLYGREEHLTTNGYRKIPG
DKCQGGVNPVREVKDLKKKCTSNFLSPEKQNSKSNSHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
UMJ	1-benzyl-3-tert-butyl-1H-pyrazole-5-carboxylic acid	C15 H18 N2 O2	1

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

Primary citation

Identification of potent inhibitors of the sortilin-progranulin interaction. Stachel, S.J., Ginnetti, A.T., Johnson, S.A. et al. Bioorg Med Chem Lett (2020) 30:127403-127403. DOI 10.1016/j.bmcl.2020.127403 · 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
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
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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