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DCN1 bound to 38

Analyse DCN1 bound to 38 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6B5Q
Type: protein
Length: 376 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DCN1-like protein 1
UniProt: Q96GG9
Ligands: CZS, 2KY, MLY, 1XY
Pockets: 5 · best druggability 0.81

Structure

x-ray diffraction · 2 distinct chains · 57% helix, 4% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DCN1-like protein 1	protein	190	58% helix, 5% strand	Q96GG9
B	DCN1-like protein 1	protein	186	56% helix, 4% strand	Q96GG9

Ligands and binding sites

CZS · 3-(6-chloro-1,3-benzothiazol-2-yl)-L-alanine · ligand · 2 copies · chains A, B
2KY · (2S)-amino(cyclopentyl)ethanoic acid · ligand · 2 copies · chains A, B
MLY · N-dimethyl-lysine · ligand · 2 copies · chains A, B
1XY · (4R)-3,4-dihydro-2H-chromen-4-amine · ligand · 2 copies · chains A, B
PPI · Propanoic acid · additive · 2 copies · chains A, B
PGE · Triethylene glycol · additive · 2 copies · chains A, B

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

Pockets

5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	969	0.81	0.82	97	PGE
2	133	0.65	0.87	23	PPI, CZS, 2KY, 1XY
3	152	0.64	0.85	25	PPI, CZS, 2KY, 1XY
4	150	0.44	0.75	21	empty
5	72	0.31	0.74	15	empty

Interfaces

1 interface between chains.

A–B · 1048 Å² buried · 21 hydrogen bonds · protein-protein

Compared structures

6B5Q · DCN1 bound to 38 · the same entry in another collection · chain A against A, TM-score 1.00
Q96GG9 · AlphaFold monomer V2.0 prediction for DCN1-like protein 1 (Q96GG9) · a predicted model of the same protein · chain B against A, TM-score 0.97

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 Q96GG9
Elsewhere: RCSB PDB 6B5Q · PDBe 6B5Q · UniProt Q96GG9

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