Research workbench

Crystal structure of PDZ-binding kinase

Analyse Crystal structure of PDZ-binding kinase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5J0A
Type: protein
Length: 602 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Lymphokine-activated killer T-cell-originated protein kinase
EC: 2.7.12.2
UniProt: Q96KB5
Ligands: HC4, SO4
Pockets: 8 · best druggability 0.59

Structure

x-ray diffraction · 2 distinct chains · 39% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Lymphokine-activated killer T-cell-originated protein kinase (EC 2.7.12.2)	protein	299	38% helix, 13% strand	Q96KB5
B	Lymphokine-activated killer T-cell-originated protein kinase (EC 2.7.12.2)	protein	303	39% helix, 13% strand	Q96KB5

Ligands and binding sites

HC4 · 4'-hydroxycinnamic acid · ligand · 4 copies · chains A, B
SO4 · Sulfate ion · ion · 10 copies · chains A, B

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

Pockets

8 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	131	0.59	0.84	25	empty
2	122	0.55	0.83	24	empty
3	301	0.54	0.75	35	empty
4	227	0.50	0.75	32	SO4
5	228	0.49	0.75	33	SO4

Interfaces

1 interface between chains.

A–B · 4772 Å² buried · 54 hydrogen bonds · protein-protein

Compared structures

5J0A · Crystal structure of PDZ-binding kinase · the same entry in another collection · chain A against A, TM-score 1.00
Q96KB5 · AlphaFold monomer V2.0 prediction for lymphokine-activated killer T-cell-originated… · a predicted model of the same protein · chain A against A, TM-score 0.77

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 Q96KB5
Elsewhere: RCSB PDB 5J0A · PDBe 5J0A · UniProt Q96KB5

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.