SMTL ID : 8q77.1

STRUCTURE OF PROTEIN KINASE CK2 CATALYTIC SUBUNIT (ISOFORM CK2ALPHA'; CSNK2A2 GENE PRODUCT) IN COMPLEX WITH THE BISUBSTRATE INHIBITOR ARC-780

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.25 Å

Oligo State

monomer

Ligands

2 x LN3: (2~{S})-2-[[(2~{S})-2-[[(2~{S})-2-[12-[[4-[[5-(4-carboxyphenyl)-1,3-thiazol-2-yl]amino]-4-oxidanylidene-butanoyl]-(2-hydroxy-2-oxoethyl)amino]dodecanoylamino]-4-oxidanyl-4-oxidanylidene-butanoyl]amino]-4-oxidanyl-4-oxidanylidene-butanoyl]amino]butanedioic acid(Non-covalent)

LN3.1: 15 residues within 4Å: Chain A: N.31, S.32, W.39, Y.41, R.95, R.170, E.195, F.196, Y.197, H.198, Q.201, E.202, Y.203, N.204 Ligands: EDO.6 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:W.39, A:W.39, A:W.39, A:F.196, A:H.198, A:Y.203 Hydrogen bonds: A:S.32, A:N.204 Water bridges: A:R.95 Salt bridges: A:R.95, A:R.170 LN3.2: 20 residues within 4Å: Chain A: R.58, K.59, L.60, G.61, R.62, V.68, V.81, K.83, I.110, F.128, E.129, Y.130, I.131, N.132, N.133, D.135, M.178, I.189, D.190, W.191 22 PLIP interactions: 22 interactions with chain A Hydrophobic interactions: A:V.81, A:I.110, A:F.128, A:F.128, A:I.189, A:I.189, A:I.189 Hydrogen bonds: A:R.62, A:R.62, A:I.131, A:I.131, A:N.133, A:D.135, A:D.190 Water bridges: A:S.66, A:Y.130, A:D.135, A:D.190, A:W.191, A:W.191 Salt bridges: A:R.62, A:K.83

6 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 10 residues within 4Å: Chain A: F.136, K.137, K.173, P.174, H.175, S.209, Y.211, F.212, E.245, P.246 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.137 EDO.4: 9 residues within 4Å: Chain A: L.100, L.103, R.104, G.105, G.106, I.109, I.110, K.111, L.112 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:L.100, A:G.105, A:L.112 Water bridges: A:G.105, A:I.109 EDO.5: 5 residues within 4Å: Chain A: V.26, Y.27, V.30, R.34, S.164 No protein-ligand interaction detected (PLIP) EDO.6: 6 residues within 4Å: Chain A: W.39, D.40, Y.41, E.42, A.43 Ligands: LN3.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.40, A:D.40, A:E.42 EDO.7: 7 residues within 4Å: Chain A: N.108, F.150, E.154, K.184, K.185, L.186, R.187 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:L.186, A:R.187 Water bridges: A:N.108, A:R.187 EDO.8: 6 residues within 4Å: Chain A: F.146, D.147, F.150, Y.151, H.181, K.184 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.151, A:K.184 Water bridges: A:D.147

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.9: 6 residues within 4Å: Chain A: A.24, Y.27, H.163, Y.226, T.329, A.330 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Werner, C. et al., Discovery and Exploration of Protein Kinase CK2 Binding Sites Using CK2alpha Cys336Ser as an Exquisite Crystallographic Tool. Kinases Phosphatases (2023)

Release Date

2023-12-06

Peptides

Casein kinase II subunit alpha': A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Casein kinase II subunit alpha'

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