SMTL ID : 5kwh.3 (2 other biounits)

Crystal structure of CK2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.12 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 6 residues within 4Å: Chain A: K.77, R.80, R.155, N.189, V.192 Ligands: SO4.6 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:N.189 Water bridges: A:K.77, A:K.77, A:R.155 Salt bridges: A:K.77, A:R.80, A:R.155 SO4.2: 3 residues within 4Å: Chain A: R.191, K.198, N.238 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.238 Water bridges: A:A.193, A:K.198 Salt bridges: A:R.191, A:K.198 SO4.3: 5 residues within 4Å: Chain A: W.33, K.75, K.102 Ligands: SO4.5, EDO.12 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:W.33 Water bridges: A:V.31, A:K.79, A:K.79, A:K.79, A:K.79 Salt bridges: A:K.75, A:K.79, A:K.102 SO4.4: 5 residues within 4Å: Chain A: R.278, K.279, R.280, R.283 Ligands: EDO.14 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.280 Water bridges: A:S.277 Salt bridges: A:R.280, A:R.283 SO4.5: 5 residues within 4Å: Chain A: K.75, K.102, R.107 Chain B: K.74 Ligands: SO4.3 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Salt bridges: A:K.75, A:K.102, A:R.107, B:K.74 SO4.6: 6 residues within 4Å: Chain A: K.74, K.76, K.77 Chain B: R.107 Ligands: SO4.1, SO4.26 7 PLIP interactions: 7 interactions with chain A Water bridges: A:K.76, A:K.77, A:K.77, A:K.77 Salt bridges: A:K.74, A:K.76, A:K.77 SO4.7: 2 residues within 4Å: Chain A: S.277, R.278 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.278 Water bridges: A:E.252, A:R.278 SO4.23: 5 residues within 4Å: Chain B: K.77, R.80, R.155, N.189, V.192 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:N.189 Water bridges: B:R.155, B:N.189 Salt bridges: B:K.77, B:R.80, B:R.155 SO4.24: 3 residues within 4Å: Chain B: K.229, H.234, R.244 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:H.234 Water bridges: B:K.229, B:K.229, B:H.234 Salt bridges: B:K.229, B:R.244 SO4.25: 5 residues within 4Å: Chain B: W.33, K.75, K.102 Ligands: SO4.26, EDO.34 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:W.33 Water bridges: B:V.31, B:K.79 Salt bridges: B:K.75, B:K.79, B:K.102 SO4.26: 6 residues within 4Å: Chain A: K.74, K.76 Chain B: K.75, K.102 Ligands: SO4.6, SO4.25 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Salt bridges: A:K.74, A:K.76, B:K.75, B:K.102 Water bridges: B:K.102 SO4.27: 5 residues within 4Å: Chain B: R.278, K.279, R.280, E.282, R.283 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:R.280 Water bridges: B:S.277, B:S.277, B:R.278 Salt bridges: B:R.280, B:R.283 SO4.28: 3 residues within 4Å: Chain B: R.191, K.198, N.238 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:N.238 Water bridges: B:R.191, A:V.105 Salt bridges: B:R.191, B:K.198

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

EDO.8: 3 residues within 4Å: Chain A: H.276, S.277, K.279 Ligand excluded by PLIP EDO.9: 7 residues within 4Å: Chain A: E.32, E.86, R.89, L.97, A.98, D.99, I.100 Ligand excluded by PLIP EDO.10: 3 residues within 4Å: Chain A: L.203, N.238, Y.239 Ligand excluded by PLIP EDO.11: 2 residues within 4Å: Chain A: D.237, N.238 Ligand excluded by PLIP EDO.12: 7 residues within 4Å: Chain A: V.31, W.33, K.75, I.78, K.79, P.109 Ligands: SO4.3 Ligand excluded by PLIP EDO.13: 4 residues within 4Å: Chain A: K.75 Chain B: K.74, K.75, K.76 Ligand excluded by PLIP EDO.14: 2 residues within 4Å: Chain A: R.280 Ligands: SO4.4 Ligand excluded by PLIP EDO.15: 2 residues within 4Å: Chain A: E.32, W.33 Ligand excluded by PLIP EDO.16: 2 residues within 4Å: Chain A: D.299, K.303 Ligand excluded by PLIP EDO.17: 4 residues within 4Å: Chain A: W.24, D.25, Y.26, E.27 Ligand excluded by PLIP EDO.18: 7 residues within 4Å: Chain A: Q.36, Y.39, L.41, V.67, V.101, D.103, A.110 Ligand excluded by PLIP EDO.19: 6 residues within 4Å: Chain A: V.248, L.249, R.278, K.279, W.281, D.302 Ligand excluded by PLIP EDO.20: 1 residues within 4Å: Chain A: Q.40 Ligand excluded by PLIP EDO.21: 2 residues within 4Å: Chain A: P.20, R.21 Ligand excluded by PLIP EDO.29: 3 residues within 4Å: Chain B: H.276, S.277, K.279 Ligand excluded by PLIP EDO.30: 6 residues within 4Å: Chain B: N.118, D.120, F.121, P.159, H.160, V.162 Ligand excluded by PLIP EDO.31: 4 residues within 4Å: Chain B: W.24, D.25, Y.26, E.27 Ligand excluded by PLIP EDO.32: 7 residues within 4Å: Chain B: Q.36, Y.39, L.41, V.67, V.101, D.103, P.104 Ligand excluded by PLIP EDO.33: 3 residues within 4Å: Chain B: K.158, H.160, S.194 Ligand excluded by PLIP EDO.34: 7 residues within 4Å: Chain B: V.31, W.33, K.75, I.78, K.79, P.109 Ligands: SO4.25 Ligand excluded by PLIP EDO.35: 7 residues within 4Å: Chain B: H.29, V.30, V.31, E.32, I.82, E.86, I.100 Ligand excluded by PLIP EDO.36: 4 residues within 4Å: Chain B: E.22, S.28, H.29, V.30 Ligand excluded by PLIP EDO.37: 5 residues within 4Å: Chain B: R.191, L.203, N.238, Y.239, F.269 Ligand excluded by PLIP EDO.38: 5 residues within 4Å: Chain B: F.232, F.233, R.244, K.247, V.248 Ligand excluded by PLIP

2 x 6XT: ~{N}-[5-[[7-(cyclopropylamino)pyrazolo[1,5-a]pyrimidin-5-yl]amino]-2-methyl-phenyl]ethanamide(Non-covalent)

6XT.22: 15 residues within 4Å: Chain A: R.47, G.48, S.51, V.53, V.66, K.68, I.95, F.113, E.114, H.115, V.116, N.118, M.163, I.174, D.175 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:V.53, A:V.53, A:K.68, A:F.113, A:N.118, A:I.174 Hydrogen bonds: A:V.116, A:V.116, A:D.175 6XT.39: 16 residues within 4Å: Chain B: L.45, R.47, G.48, S.51, V.53, V.66, K.68, I.95, E.114, H.115, V.116, N.118, H.160, M.163, I.174, D.175 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:L.45, B:L.45, B:V.53, B:V.53, B:V.66, B:K.68, B:I.174, B:D.175 Hydrogen bonds: B:V.116, B:V.116, B:D.175 Water bridges: B:L.45, B:D.175 pi-Stacking: B:H.160

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ferguson, A.D., Crystal structure of CK2. To Be Published

Release Date

2017-10-25

Peptides

Casein kinase II subunit alpha: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Casein kinase II subunit alpha

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