3S2K: PDB entry 3S2K

Structural basis of Wnt signaling inhibition by Dickkopf binding to LRP5/6. Determined by X-ray diffraction at 2.8 Å resolution. Released 2 Nov 2011.

Method: X-ray diffraction
Resolution: 2.8 Å
Organism: Homo sapiens
Chains: 3
Atoms: 10,613
Mol. weight: 157.57 kDa
Ligands: NAG
Released: 2 Nov 2011

Explore 3S2K in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3S2K contains 22 α-helices and 125 β-strands across 3 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: 7 helices, 57 β-strands

Element	Residues	Length	Sheet
β-strand	633-638	6	1
β-strand	641-646	6	1
β-strand	653-655	3	1
β-strand	664-670	7	2
β-strand	675-680	6	2
β-strand	685-690	6	2
β-strand	697-700	4	2
β-strand	709-713	5	3
β-strand	718-723	6	3
β-strand	728-733	6	3
β-strand	740-743	4	3
β-strand	750-756	7	4
β-strand	761-766	6	4
β-strand	769	1	5
β-strand	772-777	6	4
β-strand	784-787	4	4
β-strand	793-799	7	6
β-strand	804-809	6	6
β-strand	814-819	6	6
β-strand	826-829	4	6
β-strand	835-841	7	7
β-strand	844-849	6	7
β-strand	854-859	6	7
β-strand	867-871	5	7
β-strand	876-882	7	1
α-helix	884-886	3
α-helix	892-896	5
α-helix	897-899	3
β-strand	903-907	5	8
α-helix	908-910	3
β-strand	911-915	5	8
β-strand	921-922	2	9
β-strand	929-930	2	9
β-strand	935-940	6	10
β-strand	943-947	5	10
β-strand	957-958	2	10
β-strand	967-973	7	11
β-strand	978-983	6	11
β-strand	988-993	6	11
β-strand	1000-1003	4	11
β-strand	1016-1022	7	12
β-strand	1027-1032	6	12
β-strand	1038-1042	5	12
β-strand	1047-1052	6	12
β-strand	1059-1065	7	13
α-helix	1066-1068	3
β-strand	1070-1076	7	13
β-strand	1081-1087	7	13
β-strand	1094-1097	4	13
β-strand	1104-1110	7	14
β-strand	1115-1120	6	14
β-strand	1125-1130	6	14
β-strand	1137-1140	4	14
β-strand	1147-1153	7	15
β-strand	1156-1161	6	15
β-strand	1166-1171	6	15
β-strand	1178-1182	5	15
β-strand	1188-1194	7	10
α-helix	1199-1202	4
α-helix	1209-1213	5
β-strand	1217-1220	4	16
β-strand	1226-1229	4	16
β-strand	1235-1236	2	17
β-strand	1243-1244	2	17

Chain B: 11 helices, 57 β-strands

Element	Residues	Length	Sheet
α-helix	631-632	2
β-strand	633-638	6	18
β-strand	639	1	19
β-strand	641-645	5	18
β-strand	654-655	2	18
β-strand	664-670	7	19
β-strand	675-680	6	19
β-strand	685-690	6	19
β-strand	697-700	4	19
β-strand	709-713	5	20
β-strand	718-723	6	20
β-strand	728-733	6	20
β-strand	740-743	4	20
β-strand	750-756	7	21
β-strand	761-766	6	21
β-strand	772-777	6	21
β-strand	784-787	4	21
β-strand	793-799	7	22
β-strand	804-809	6	22
β-strand	814-819	6	22
β-strand	826-829	4	22
β-strand	835-841	7	23
β-strand	844-849	6	23
β-strand	854-859	6	23
β-strand	867-871	5	23
β-strand	879-882	4	18
α-helix	884-886	3
α-helix	892-894	3
α-helix	896-899	4
β-strand	903-906	4	24
β-strand	912-915	4	24
α-helix	920	1
β-strand	921-922	2	25
α-helix	923	1
β-strand	929-930	2	25
β-strand	935-940	6	26
β-strand	944-947	4	26
α-helix	954-956	3
β-strand	957-958	2	26
β-strand	967-973	7	27
β-strand	978-983	6	27
β-strand	988-992	5	27
β-strand	1000-1003	4	27
β-strand	1016-1022	7	28
β-strand	1027-1032	6	28
β-strand	1037-1042	6	28
β-strand	1047-1053	7	28
β-strand	1059-1065	7	29
β-strand	1070-1077	8	29
β-strand	1080-1087	8	29
β-strand	1094-1097	4	29
β-strand	1104-1110	7	30
β-strand	1115-1120	6	30
β-strand	1125-1130	6	30
β-strand	1137-1140	4	30
β-strand	1147-1153	7	31
β-strand	1156-1161	6	31
β-strand	1166-1171	6	31
α-helix	1177-1178	2
β-strand	1179-1182	4	31
β-strand	1188-1194	7	26
α-helix	1195-1197	3
α-helix	1199-1203	5
α-helix	1210-1213	4
β-strand	1217-1220	4	32
β-strand	1226-1229	4	32
β-strand	1235-1236	2	33
β-strand	1243-1244	2	33

Chain C: 4 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	183	1	34
β-strand	188	1	35
α-helix	192-194	3
β-strand	195	1	34
β-strand	199-204	6	35
β-strand	207-212	6	35
α-helix	213	1
β-strand	214	1	36
β-strand	219	1	5
α-helix	226-231	6
β-strand	234	1	35
α-helix	235-238	4
β-strand	239	1	36
β-strand	243-247	5	5
β-strand	261-265	5	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Low-density lipoprotein receptor-related protein 6	A, B	protein	629	Homo sapiens	O75581 (AlphaFold model)
Dickkopf-related protein 1	C	protein	97	Homo sapiens	O94907 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>3S2K_1 Low-density lipoprotein receptor-related protein 6 (chains A, B)
ADPEAFLLFSRRADIRRISLETNNNNVAIPLTGVKEASALDFDVTDNRIYWTDISLKTIS
RAFMNGSALEHVVEFGLDYPEGMAVDWLGKNLYWADTGTNRIEVSKLDGQHRQVLVWKDL
DSPRALALDPAEGFMYWTEWGGKPKIDRAAMDGSERTTLVPNVGRANGLTIDYAKRRLYW
TDLDTNLIESSNMLGLNREVIADDLPHPFGLTQYQDYIYWTDWSRRSIERANKTSGQNRT
IIQGHLDYVMDILVFHSSRQSGWNECASSNGHCSHLCLAVPVGGFVCGCPAHYSLNADNR
TCSAPTTFLLFSQKSAINRMVIDEQQSPDIILPIHSLRNVRAIDYDPLDKQLYWIDSRQN
MIRKAQEDGSQGFTVVVSSVPSQNLEIQPYDLSIDIYSRYIYWTCEATNVINVTRLDGRS
VGVVLKGEQDRPRAIVVNPEKGYMYFTNLQERSPKIERAALDGTEREVLFFSGLSKPIAL
ALDSRLGKLFWADSDLRRIESSDLSGANRIVLEDSNILQPVGLTVFENWLYWIDKQQQMI
EKIDMTGREGRTKVQARIAQLSDIHAVKELNLQEYRQHPCAQDNGGCSHICLVKGDGTTR
CSCPMHLVLLQDELSCGEPHHHHHHHHHH

Sequence of entity 2 (C), FASTA

>3S2K_2 Dickkopf-related protein 1 (chains C)
ADPMYHTKGQEGSVCLRSSDCASGLCCARHFWSKICKPVLKEGQVCTKHRRKGSHGLEIF
QRCYCGEGLSCRIQKDHHQASNSSRLHTCQRHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	6

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

Primary citation

Structural Basis of Wnt Signaling Inhibition by Dickkopf Binding to LRP5/6. Ahn, V.E., Chu, M.L., Choi, H.J. et al. Dev Cell (2011) 21:862-873. DOI 10.1016/j.devcel.2011.09.003 · PubMed

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

About this viewer

MolViewer shows 3S2K directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.