MolNFT v1 · #111361 · protein

Structure of sad kinase

4YOM · SERINE/THREONINE-protein kinase BRSK2: “Structure of sad kinase”. X-ray diffraction, 5 pockets (best druggability 0.72). MolNFT v1 #111361 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4YOM
Type: protein
Length: 426 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: SERINE/THREONINE-protein kinase BRSK2
EC: 2.7.11.26
UniProt: Q69Z98
Pockets: 5 · best druggability 0.72

Structure

x-ray diffraction · 2 distinct chains · 39% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B	SERINE/THREONINE-protein kinase BRSK2 (EC 2.7.11.26)	protein	322	42% helix, 14% strand	Q69Z98
A	SERINE/THREONINE-protein kinase BRSK2 (EC 2.7.11.26)	protein	104	28% helix, 38% strand	Q69Z98

Ligands and binding sites

EDO · 1,2-ethanediol · additive · 2 copies · chains B, A

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

Pockets

5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	637	0.72	0.79	57	empty
2	182	0.58	0.81	23	empty
3	238	0.57	0.79	36	empty
4	120	0.50	0.80	23	empty
5	77	0.35	0.76	14	EDO

Interfaces

1 interface between chains.

B–A · 1290 Å² buried · 10 hydrogen bonds · protein-protein

Compared structures

4YOM · Structure of SAD kinase · the same entry in another collection · chain B against B, TM-score 1.00
Q69Z98 · AlphaFold monomer V2.0 prediction for SERINE/THREONINE-protein kinase BRSK2 (Q69Z98) · a predicted model of the same protein · chain A against A, TM-score 0.89

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 Q69Z98
Elsewhere: RCSB PDB 4YOM · PDBe 4YOM · UniProt Q69Z98

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