5LNP: PDB entry 5LNP

Domain-swapped dimer of human Dishevelled2 DEP domain: monoclinic crystal form crystallised from monomeric fraction. Determined by X-ray diffraction at 1.99 Å resolution. Released 12 Oct 2016.

Method: X-ray diffraction
Resolution: 1.99 Å
Organism: Homo sapiens
Chains: 4
Atoms: 3,031
Mol. weight: 43.53 kDa
Released: 12 Oct 2016

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

Secondary structure: helices and β-sheets

5LNP contains 12 α-helices and 28 β-strands across 4 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: 3 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	418	1	1
α-helix	423-430	8
β-strand	440-447	8	2
β-strand	452	1	3
β-strand	453-454	2	4
α-helix	455-465	11
β-strand	467	1	5
α-helix	472-484	13
β-strand	488-490	3	4
β-strand	502-505	4	4

Chains B and C: 3 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	418	1	5
α-helix	423-431	9
β-strand	440	1	3
β-strand	443-452	10	2
β-strand	453-454	2	6
α-helix	455-465	11
β-strand	467	1	1
α-helix	472-484	13
β-strand	488-490	3	6
β-strand	502-505	4	6

Chain D: 3 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	418	1	11
α-helix	423-431	9
β-strand	440-447	8	9
β-strand	452	1	8
β-strand	453-454	2	12
α-helix	455-465	11
β-strand	467	1	7
α-helix	472-484	13
β-strand	488-490	3	12
β-strand	502-505	4	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Segment polarity protein dishevelled homolog DVL-2	A, C, D	protein	97	Homo sapiens	O14641 (AlphaFold model)
Segment polarity protein dishevelled homolog DVL-2	B	protein	97	Homo sapiens	O14641 (AlphaFold model)

Sequence of entity 1 (A, C, D), FASTA

>5LNP_1 Segment polarity protein dishevelled homolog DVL-2 (chains A, C, D)
SSGLSVHTDMASVTKAMAAPESGLEVRDRMWLKITIPNAFLGSDVVDWLYHHVEGFPERR
EARKYASGLLKAGLIRHTVNKITFSEQCYYVFGDLSG

Sequence of entity 2 (B), FASTA

>5LNP_2 Segment polarity protein dishevelled homolog DVL-2 (chains B)
SSGLSVHTDMASVTKAMAAPESGLEVRDRMWLKITIPNAFLGSDVVDWLYHHVEGFPERR
EARKYASGLLKAGLIRHTVNKITFSEQCYYVFGDLSG

Primary citation

Wnt Signalosome Assembly by DEP Domain Swapping of Dishevelled. Gammons, M.V., Renko, M., Johnson, C.M. et al. Mol Cell (2016) 64:92-104. DOI 10.1016/j.molcel.2016.08.026 · PubMed

Other PDB entries of the same protein (UniProt O14641 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3CBZ 1.38 Å, The Dvl2 PDZ Domain in Complex with the N2 Inhibitory Peptide
3CBY 1.5 Å, The Dvl2 PDZ Domain in Complex with the N1 Inhibitory Peptide
2REY 1.55 Å, Crystal structure of the PDZ domain of human dishevelled 2 (homologous to Drosophila dsh)
6IW3 1.64 Å, High resolution structure of Dvl2-DIX Y27W/C80S mutant
3CBX 1.7 Å, The Dvl2 PDZ Domain in Complex with the C1 Inhibitory Peptide
3CC0 1.75 Å, The Dvl2 PDZ Domain in Complex with the N3 Inhibitory Peptide
8WWR 1.75 Å, Crystal structure of apo human dishevelled 2 (Dvl2) PDZ domain
5SUZ 1.84 Å, Domain-swapped dimer of human Dishevelled2 DEP domain: C-centered monoclinic crystal…
5SUY 1.88 Å, Domain-swapped dimer of human Dishevelled2 DEP domain: monoclinic crystal form…
35UG 1.95 Å, Human DVL2 PDZ domain in complex with Vangl2
4WIP 2.69 Å, DIX domain of human Dvl2
8YR7 3.0 Å, Crystal structure of human dishevelled 2 (Dvl2) PDZ domain fused with WGEF internal…

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