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Crystal structure of S. cerevisiae DCN1

Analyse Crystal structure of S. cerevisiae DCN1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3BQ3
Type: protein
Length: 250 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Defective in cullin neddylation protein 1
UniProt: Q12395
Pockets: 3 · best druggability 0.51

Structure

x-ray diffraction · 1 distinct chain · 65% helix, 3% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Defective in cullin neddylation protein 1	protein	250	65% helix, 3% strand	Q12395

Ligands and binding sites

GOL · Glycerol · additive · chains A

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

Pockets

3 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	228	0.51	0.75	24	empty
2	79	0.39	0.77	17	empty
3	77	0.37	0.77	15	empty

Modifications

Observed in the structure: 4 modified (engineered).

Compared structures

3BQ3 · Crystal structure of S. cerevisiae Dcn1 · the same entry in another collection · chain A against A, TM-score 1.00
Q12395 · AlphaFold monomer V2.0 prediction for defective in cullin neddylation protein 1 (Q12395) · a predicted model of the same protein · chain A against A, TM-score 0.79

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 Q12395
Elsewhere: RCSB PDB 3BQ3 · PDBe 3BQ3 · UniProt Q12395

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