MolNFT v1 · #59904 · protein

The DVL2 PDZ domain in complex with the N1 inhibitory peptide

3CBY · Dishevelled-2: “The DVL2 PDZ domain in complex with the N1 inhibitory peptide”. X-ray diffraction, 1 pocket (best druggability 0.41). MolNFT v1 #59904 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3CBY
Type: protein
Length: 199 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Dishevelled-2
UniProt: O14641
Pockets: 1 · best druggability 0.41

Structure

x-ray diffraction · 2 distinct chains · 19% helix, 37% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Dishevelled-2	protein	101	20% helix, 36% strand	O14641
B	Dishevelled-2	protein	98	17% helix, 38% strand	O14641

Ligands and binding sites

EDO · 1,2-ethanediol · additive · 2 copies · chains A, B

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

Pockets

1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	68	0.41	0.80	18	EDO

Interfaces

1 interface between chains.

A–B · 1439 Å² buried · 35 hydrogen bonds · protein-protein

Compared structures

3CBY · The Dvl2 PDZ Domain in Complex with the N1 Inhibitory Peptide · the same entry in another collection · chain A against A, 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 A against A, TM-score 0.83

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 3CBY · PDBe 3CBY · UniProt O14641

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