SMTL ID : 6z19.1

Crystal structure of P8C9 bound to CK2alpha

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.47 Å

Oligo State

monomer

Ligands

1 x ALA- LEU- TYR- GLY- PHE- LYS- TRP- ALA: P2(Non-covalent)

ALA-LEU-TYR-GLY-PHE-LYS-TRP-ALA.1: 16 residues within 4Å: Chain A: Q.35, Y.38, Q.39, L.40, V.41, R.42, K.43, E.51, F.53, V.66, I.68, K.70, V.100, D.102, T.107, A.109 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:Q.35, A:L.40, A:L.40, A:L.40, A:F.53, A:F.53, A:V.66, A:I.68, A:I.68, A:V.100, A:T.107, A:A.109 Hydrogen bonds: A:Q.35, A:L.40, A:L.40, A:K.70 Water bridges: A:D.102

1 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.2: 15 residues within 4Å: Chain A: L.44, S.50, V.52, V.65, K.67, I.94, E.113, V.115, H.159, N.160, M.162, I.173, D.174 Ligands: MG.6, MG.7 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:S.50, A:E.113, A:V.115, A:D.174, A:D.174 Water bridges: A:D.155, A:H.159, A:N.160, A:N.160, A:D.174 Salt bridges: A:K.67, A:K.67

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.3: 3 residues within 4Å: Chain A: K.157, H.159 Ligands: ACT.4 3 PLIP interactions: 3 interactions with chain A Water bridges: A:K.157 Salt bridges: A:K.157, A:H.159 ACT.4: 5 residues within 4Å: Chain A: D.155, K.157, S.193 Ligands: ACT.3, PEG.8 2 PLIP interactions: 2 interactions with chain A Water bridges: A:N.160 Salt bridges: A:K.157

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 6 residues within 4Å: Chain A: E.85, R.88, L.96, A.97, D.98, I.99 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:E.85, A:R.88, A:R.88, A:A.97, A:D.98 Water bridges: A:I.99 GOL.14: 5 residues within 4Å: Chain A: R.279, W.280, E.281, L.297, D.298 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:W.280, A:L.297, A:D.298 GOL.15: 4 residues within 4Å: Chain A: D.236, Y.238, D.239, I.271 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.239 Water bridges: A:D.239

2 x MG: MAGNESIUM ION(Non-covalent)

MG.6: 4 residues within 4Å: Chain A: N.160, D.174 Ligands: ADP.2, MG.7 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.174, H2O.4, H2O.5 MG.7: 3 residues within 4Å: Chain A: D.174 Ligands: ADP.2, MG.6 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.174, A:D.174, H2O.1, H2O.2, H2O.7

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.8: 7 residues within 4Å: Chain A: L.177, R.190, V.191, A.192, K.197, N.237 Ligands: ACT.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.192, A:N.237

4 x SO4: SULFATE ION(Non-functional Binders)

SO4.9: 1 residues within 4Å: Chain A: R.88 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.88, A:R.88 Salt bridges: A:R.88 SO4.10: 6 residues within 4Å: Chain A: K.76, R.79, R.154, L.177, N.188, V.191 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.188 Water bridges: A:R.154, A:N.188 Salt bridges: A:K.76, A:R.79, A:R.154 SO4.11: 2 residues within 4Å: Chain A: R.243, K.246 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.243, A:K.246 SO4.12: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

1 x NA: SODIUM ION(Non-functional Binders)

NA.13: 1 residues within 4Å: Chain A: E.21 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.21

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Atkinson, E.L. et al., Development of small cyclic peptides targeting the CK2 alpha / beta interface. Chem.Commun.(Camb.) (2022)

Release Date

2021-05-26

Peptides

Casein kinase II subunit alpha: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Casein kinase II subunit alpha