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The wd domain ofarabidopsis thaliana E3 ubiquitin ligase COP1 in complex with peptide from HY5

Analyse The wd domain ofarabidopsis thaliana E3 ubiquitin ligase COP1 in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5KWN
Type: protein
Length: 315 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: E3 ubiquitin-protein ligase COP1; Peptide 16-mer
EC: 6.3.2.-
UniProt: P43254
Pockets: 2 · best druggability 0.74

Structure

x-ray diffraction · 2 distinct chains · 3% helix, 50% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	E3 ubiquitin-protein ligase COP1 (EC 6.3.2.-)	protein	306	3% helix, 51% strand	P43254
U	Peptide 16-mer	protein	9	0% helix, 11% strand	—

Pockets

2 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	420	0.74	0.84	51	empty
2	88	0.41	0.78	20	empty

Interfaces

1 interface between chains.

A–U · 734 Å² buried · 9 hydrogen bonds · protein-protein

Compared structures

5KWN · The WD domain ofArabidopsis thaliana E3 Ubiquitin Ligase COP1 in complex with peptide… · the same entry in another collection · chain A against A, TM-score 1.00
P43254 · AlphaFold monomer V2.0 prediction for E3 ubiquitin-protein ligase COP1 (P43254) · a predicted model of the same protein · chain A against A, TM-score 1.00

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 P43254
Elsewhere: RCSB PDB 5KWN · PDBe 5KWN · UniProt P43254

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