MolNFT v1 · #108809 · protein

Dix domain of human DVL2

4WIP · Segment polarity protein dishevelled homolog dvl-2: “Dix domain of human DVL2”. X-ray diffraction, 4 pockets (best druggability 0.41). MolNFT v1 #108809 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4WIP
Type: protein
Length: 243 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Segment polarity protein dishevelled homolog dvl-2
UniProt: O14641
Pockets: 4 · best druggability 0.41

Structure

x-ray diffraction · 2 distinct chains · 10% helix, 46% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Segment polarity protein dishevelled homolog dvl-2	protein	81	10% helix, 46% strand	O14641
C	Segment polarity protein dishevelled homolog dvl-2	protein	81	10% helix, 46% strand	O14641

Ligands and binding sites

1PE · Pentaethylene glycol · additive · 3 copies · chains A, B, C

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	141	0.41	0.74	25	empty
2	79	0.37	0.77	19	1PE
3	57	0.32	0.76	14	1PE
4	66	0.31	0.74	14	empty

Interfaces

2 interfaces between chains.

A–B · 530 Å² buried · 7 hydrogen bonds · protein-protein
B–C · 463 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

4WIP · DIX domain of human Dvl2 · the same entry in another collection · chain B against B, 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 0.96

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 4WIP · PDBe 4WIP · UniProt O14641

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