4DG6: Domains 1 and 2 of LRP6

Crystal structure of domains 1 and 2 of LRP6. Determined by X-ray diffraction at 2.9 Å resolution. Released 13 Jun 2012.

Method: X-ray diffraction
Resolution: 2.9 Å
Organism: Homo sapiens
Chains: 1
Atoms: 5,005
Mol. weight: 71.07 kDa
Ligands: PO4
Released: 13 Jun 2012

Explore 4DG6 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4DG6 contains 4 α-helices and 59 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: 4 helices, 59 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	1
β-strand	9	1	2
β-strand	12-15	4	1
β-strand	25	1	1
β-strand	34-40	7	2
β-strand	45-50	6	2
β-strand	55-60	6	2
β-strand	67-71	5	2
β-strand	80-84	5	3
β-strand	89-94	6	3
β-strand	99-104	6	3
β-strand	111-114	4	3
β-strand	121-127	7	4
β-strand	132-137	6	4
β-strand	143-148	6	4
β-strand	155-158	4	4
β-strand	165-171	7	5
β-strand	176-181	6	5
β-strand	188-191	4	5
β-strand	198-199	2	5
β-strand	211-213	3	6
β-strand	217-222	6	6
β-strand	227-232	6	6
β-strand	252-254	3	1
α-helix	257-259	3
β-strand	277-280	4	7
β-strand	287-290	4	7
β-strand	297	1	8
β-strand	304	1	8
β-strand	310-316	7	9
β-strand	320-324	5	9
β-strand	335-336	2	9
β-strand	343-349	7	10
β-strand	354-359	6	10
β-strand	364-368	5	10
β-strand	376-379	4	10
β-strand	388-392	5	11
β-strand	397-402	6	11
β-strand	407-412	6	11
β-strand	419-423	5	11
β-strand	428-435	8	12
β-strand	440-446	7	12
β-strand	451-456	6	12
β-strand	463-466	4	12
β-strand	473-476	4	13
β-strand	479	1	14
α-helix	480-482	3
β-strand	484	1	14
β-strand	487-489	3	13
β-strand	494-497	4	13
β-strand	499	1	14
β-strand	506-510	5	13
β-strand	519-522	4	15
β-strand	525-529	5	15
β-strand	536-540	5	15
β-strand	548-550	3	15
β-strand	556-563	8	9
α-helix	572-574	3
α-helix	576-579	4
β-strand	583-585	3	16
β-strand	592-594	3	16
β-strand	600-601	2	17
β-strand	608-609	2	17

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Low-density lipoprotein receptor-related protein 6	A	protein	616	Homo sapiens	O75581 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>4DG6_1 Low-density lipoprotein receptor-related protein 6 (chains A)
APLLLYANRRDLRLVDATNGKENATIVVGGLEDAAAVDFVFSHGLIYWSDVSEEAIKRTE
FNKTESVQNVVVSGLLSPDGLACDWLGEKLYWTDSETNRIEVSNLDGSLRKVLFWQELDQ
PRAIALDPSSGFMYWTDWGEVPKIERAGMDGSSRFIIINSEIYWPNGLTLDYEEQKLYWA
DAKLNFIHKSNLDGTNRQAVVKGSLPHPFALTLFEDILYWTDWSTHSILACNKYTGEGLR
EIHSDIFSPMDIHAFSQQRQPNATNPCGIDNGGCSHLCLMSPVKPFYQCACPTGVKLLEN
GKTCKDGATELLLLARRTDLRRISLDTPDFTDIVLQLEDIRHAIAIDYDPVEGYIYWTDD
EVRAIRRSFIDGSGSQFVVTAQIAHPDGIAVDWVARNLYWTDTGTDRIEVTRLNGTMRKI
LISEDLEEPRAIVLDPMVGYMYWTDWGEIPKIERAALDGSDRVVLVNTSLGWPNGLALDY
DEGKIYWGDAKTDKIEVMNTDGTGRRVLVEDKIPHIFGFTLLGDYVYWTDWQRRSIERVH
KRSAEREVIIDQLPDLMGLKATNVHRVIGSNPCAEENGGCSHLCLYRPQGLRCACPIGFE
LISDMKTCIVPEAFLL

Ligands and cofactors

ID	Name	Formula	Copies
PO4	Phosphate ion	O4 P	2

Primary citation

Characterization of the interaction of sclerostin with the LRP family of Wnt co-receptors. Holdsworth, G., Slocombe, P., Doyle, C. et al. To be published.

Other PDB entries of the same protein (UniProt O75581 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3SOV 1.27 Å, The structure of a beta propeller domain in complex with peptide S
7NAM 1.6 Å, LRP6_E1 in complex with Lr-EET-3.5
8FFE 1.72 Å, Crystal structure of LRP6 E1E2 domains bound to YW210.09 Fab and engineered XWnt8 peptide
3SOB 1.9 Å, The structure of the first YWTD beta propeller domain of LRP6 in complex with a FAB
3SOQ 1.9 Å, The structure of the first YWTD beta propeller domain of LRP6 in complex with a DKK1…
4A0P 1.9 Å, Crystal structure of LRP6P3E3P4E4
8DVM 2.0 Å, Crystal structure of LRP6 E3E4 in complex with disulfide constrained peptide E3.6
4NM5 2.3 Å, Crystal structure of GSK-3/Axin complex bound to phosphorylated Wnt receptor LRP6 c-motif
4NM7 2.3 Å, Crystal structure of GSK-3/Axin complex bound to phosphorylated Wnt receptor LRP6 e-motif
8DVL 2.5 Å, Crystal structure of LRP6 E3E4 in complex with disulfide constrained peptide E3.18
5AIR 2.53 Å, Structural analysis of mouse GSK3beta fused with LRP6 peptide.
8DVN 2.53 Å, Crystal structure of LRP6 E3E4 in complex with disulfide constrained peptide E3.10

Browse structure collections

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