MolNFT v1 · #155269 · protein

Crystal structure of CK2A2 with hematein

6L20 · Casein kinase II subunit alpha': “Crystal structure of CK2A2 with hematein”. X-ray diffraction, 2 ligands (E3U, CL), 11 pockets (best druggability 0.76). MolNFT v1 #155269 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 6L20
Type: protein
Length: 1,259 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Casein kinase II subunit alpha'
EC: 2.7.11.1
UniProt: P19784
Ligands: E3U, CL
Pockets: 11 · best druggability 0.76

Structure

x-ray diffraction · 4 distinct chains · 37% helix, 12% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Casein kinase II subunit alpha' (EC 2.7.11.1)	protein	313	38% helix, 12% strand	P19784
D	Casein kinase II subunit alpha' (EC 2.7.11.1)	protein	313	35% helix, 10% strand	P19784
G	Casein kinase II subunit alpha' (EC 2.7.11.1)	protein	319	32% helix, 13% strand	P19784
J	Casein kinase II subunit alpha' (EC 2.7.11.1)	protein	314	41% helix, 12% strand	P19784

Ligands and binding sites

E3U · (6AR)-3,4,6A,10-tetrakis(oxidanyl)-6,7-dihydroindeno[2, 1-c]chromen-9-one · ligand · 4 copies · chains A, D, G, J
CL · Chloride ion · ion · 2 copies · chains A, D

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

Pockets

11 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	683	0.76	0.82	73	empty
2	526	0.74	0.82	58	CL
3	667	0.72	0.79	66	empty
4	157	0.62	0.84	20	E3U
5	192	0.61	0.82	24	E3U

Interfaces

4 interfaces between chains.

A–G · 643 Å² buried · 5 hydrogen bonds · protein-protein
D–J · 621 Å² buried · 4 hydrogen bonds · protein-protein
D–G · 172 Å² buried · 8 hydrogen bonds · protein-protein
A–D · 21 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

6L20 · Crystal structure of CK2a2 with hematein · the same entry in another collection · chain J against J, TM-score 1.00
P19784 · AlphaFold monomer V2.0 prediction for casein kinase II subunit alpha' (P19784) · a predicted model of the same protein · chain D against A, TM-score 0.99

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 P19784
Elsewhere: RCSB PDB 6L20 · PDBe 6L20 · UniProt P19784

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