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Domain-swapped dimer of human DISHEVELLED2 dep domain: monoclinic crystal form crystallised from monomeric fraction

Analyse Domain-swapped dimer of human DISHEVELLED2 dep domain: monoclinic crystal form… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5LNP
Type: protein
Length: 377 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Segment polarity protein dishevelled homolog dvl-2
UniProt: O14641
Ligands: SO4
Pockets: 2 · best druggability 0.75

Structure

x-ray diffraction · 2 distinct chains · 34% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, D	Segment polarity protein dishevelled homolog dvl-2	protein	94	34% helix, 21% strand	O14641
C	Segment polarity protein dishevelled homolog dvl-2	protein	95	35% helix, 23% strand	O14641

Ligands and binding sites

SO4 · Sulfate ion · ion · chains C

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1164	0.75	0.77	95	empty
2	182	0.49	0.76	37	empty

Interfaces

6 interfaces between chains.

C–D · 2657 Å² buried · 30 hydrogen bonds · protein-protein
A–B · 2623 Å² buried · 25 hydrogen bonds · protein-protein
A–C · 318 Å² buried · 3 hydrogen bonds · protein-protein
B–C · 279 Å² buried · 3 hydrogen bonds · protein-protein
A–D · 191 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 modified (oxidation).

Compared structures

5LNP · Domain-swapped dimer of human Dishevelled2 DEP domain: monoclinic crystal form… · the same entry in another collection · chain D against D, TM-score 1.00
O14641 · AlphaFold monomer V2.0 prediction for segment polarity protein dishevelled homolog dvl-2… · a predicted model of the same protein · chain C against A, TM-score 0.69

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt O14641
Elsewhere: RCSB PDB 5LNP · PDBe 5LNP · UniProt O14641

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