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Xenopus dishevelled PDZ domain

Analyse Xenopus dishevelled PDZ domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1L6O
Type: protein
Length: 304 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Segment polarity protein dishevelled homolog dvl- 2; Dapper 1
UniProt: P51142
Pockets: 1 · best druggability 0.67

Structure

x-ray diffraction · 4 distinct chains · 17% helix, 36% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Segment polarity protein dishevelled homolog dvl- 2	protein	95	18% helix, 35% strand	P51142
B	Segment polarity protein dishevelled homolog dvl- 2	protein	93	23% helix, 33% strand	P51142
C	Segment polarity protein dishevelled homolog dvl- 2	protein	92	13% helix, 38% strand	P51142
D, E, F	Dapper 1	protein	8	0% helix, 75% strand	—

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	447	0.67	0.79	59	empty

Interfaces

11 interfaces between chains.

B–E · 527 Å² buried · 10 hydrogen bonds · protein-protein
C–F · 518 Å² buried · 10 hydrogen bonds · protein-protein
A–D · 512 Å² buried · 11 hydrogen bonds · protein-protein
A–E · 312 Å² buried · 4 hydrogen bonds · protein-protein
A–B · 289 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 15 modified (engineered).

Compared structures

1L6O · Xenopus dishevelled PDZ domain · the same entry in another collection · chain F against F, TM-score 1.00
P51142 · 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 0.92

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 P51142
Elsewhere: RCSB PDB 1L6O · PDBe 1L6O · UniProt P51142

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