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Crystal structure of the kelch domain of human KLHL20 in complex with DAPK1 peptide

Analyse Crystal structure of the kelch domain of human KLHL20 in complex with DAPK1… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6GY5
Type: protein
Length: 296 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Kelch-like protein 20; Death-associated protein kinase 1
UniProt: Q9Y2M5
Ligands: NA, CL
Pockets: 1 · best druggability 0.74

Structure

x-ray diffraction · 2 distinct chains · 0% helix, 48% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Kelch-like protein 20	protein	285	0% helix, 50% strand	Q9Y2M5
U	Death-associated protein kinase 1	protein	11	0% helix, 0% strand	—

Ligands and binding sites

NA · Sodium ion · metal · 14 copies · chains A, U
CL · Chloride ion · ion · chains A
EDO · 1,2-ethanediol · additive · 9 copies · chains A, U

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	385	0.74	0.85	38	NA

Interfaces

1 interface between chains.

A–U · 540 Å² buried · 12 hydrogen bonds · protein-protein

Compared structures

6GY5 · Crystal structure of the kelch domain of human KLHL20 in complex with DAPK1 peptide · the same entry in another collection · chain A against A, TM-score 1.00
Q9Y2M5 · AlphaFold monomer V2.0 prediction for kelch-like protein 20 (Q9Y2M5) · a predicted model of the same protein · chain A against A, TM-score 0.99

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Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt Q9Y2M5
Elsewhere: RCSB PDB 6GY5 · PDBe 6GY5 · UniProt Q9Y2M5

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