MolNFT v1 · #161086 · protein

The crystal structure of CK2A bound to P1-C4

6Q38 · Casein kinase II subunit alpha: “The crystal structure of CK2A bound to P1-C4”. X-ray diffraction, 2 ligands (HEK, BEZ), 2 pockets (best druggability 0.71). MolNFT v1 #161086 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 6Q38
Type: protein
Length: 335 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Casein kinase II subunit alpha; Stapled peptide
EC: 2.7.11.1
UniProt: P68400
Ligands: HEK, BEZ
Pockets: 2 · best druggability 0.71

Structure

x-ray diffraction · 2 distinct chains · 39% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Casein kinase II subunit alpha (EC 2.7.11.1)	protein	327	39% helix, 16% strand	P68400
C	Stapled peptide	protein	8	0% helix, 38% strand	—

Ligands and binding sites

HEK · 3-[1-[(2~{S})-2-(2-acetamidoethanoylamino)-3-oxidanylidene-propyl]-1,2,3-triazol-4-yl]-5-[1-[(2~{S})-2-azanyl-3-[[2-[(2-azanyl-2-oxidanylidene-ethyl)amino]-2-oxidanylidene-ethyl]amino]-3-oxidanylidene-propyl]-1,2,3-triazol-4-yl]benzoic acid · ligand · chains C
BEZ · Benzoic acid · ligand · chains A

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

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	353	0.71	0.83	49	BEZ
2	52	0.28	0.75	12	empty

Interfaces

1 interface between chains.

A–C · 560 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 covalent (covalent ligand).

Compared structures

6Q38 · The Crystal structure of CK2a bound to P1-C4 · the same entry in another collection · chain A against A, TM-score 1.00
P68400 · AlphaFold monomer V2.0 prediction for casein kinase II subunit alpha (P68400) · a predicted model of the same protein · chain A 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 P68400
Elsewhere: RCSB PDB 6Q38 · PDBe 6Q38 · UniProt P68400

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