SMTL ID : 4lfi.1

Crystal structure of scCK2 alpha in complex with GMPPNP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-dimer

Ligands

2 x GNP: PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER(Non-covalent)

GNP.1: 23 residues within 4Å: Chain A: V.48, G.49, R.50, G.51, K.52, Y.53, S.54, V.56, V.69, K.71, E.155, V.157, N.159, D.197, K.199, H.201, N.202, M.204, I.215, D.216 Ligands: MN.2, MN.3, GOL.4 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:K.52, A:Y.53, A:S.54, A:K.71, A:V.157, A:V.157, A:V.157, A:N.159, A:K.199 Water bridges: A:K.199, A:H.201, A:N.202, A:S.235 Salt bridges: A:K.71 GNP.10: 23 residues within 4Å: Chain B: V.48, G.49, R.50, G.51, K.52, Y.53, S.54, V.56, V.69, K.71, E.155, V.157, N.159, D.197, K.199, H.201, N.202, M.204, I.215, D.216 Ligands: MN.11, MN.12, GOL.13 17 PLIP interactions: 17 interactions with chain B Hydrogen bonds: B:K.52, B:Y.53, B:S.54, B:K.71, B:V.157, B:V.157, B:V.157, B:N.159, B:D.197, B:K.199, B:N.202 Water bridges: B:Y.156, B:N.159, B:H.201, B:H.201, B:N.202 Salt bridges: B:K.71

4 x MN: MANGANESE (II) ION(Non-covalent)

MN.2: 4 residues within 4Å: Chain A: N.202, D.216 Ligands: GNP.1, MN.3 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.216, H2O.1 MN.3: 4 residues within 4Å: Chain A: Y.53, D.216 Ligands: GNP.1, MN.2 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.216, A:D.216, H2O.2, H2O.2 MN.11: 4 residues within 4Å: Chain B: Y.53, D.216 Ligands: GNP.10, MN.12 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.216, B:D.216, H2O.12, H2O.13 MN.12: 4 residues within 4Å: Chain B: N.202, D.216 Ligands: GNP.10, MN.11 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.216, H2O.11

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 4 residues within 4Å: Chain A: V.48, N.159, D.161 Ligands: GNP.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.159, A:D.161, A:D.161 Water bridges: A:F.162 GOL.13: 4 residues within 4Å: Chain B: V.48, N.159, D.161 Ligands: GNP.10 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.159, B:D.161 Water bridges: B:F.162

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

SO4.5: 4 residues within 4Å: Chain A: R.83, R.196, L.219, N.230 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.230 Water bridges: A:R.196, A:E.221 Salt bridges: A:K.80, A:R.83, A:R.196 SO4.6: 3 residues within 4Å: Chain A: R.232, R.236, N.279 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:N.279 Water bridges: A:R.232, A:R.232, A:N.279, A:N.279 Salt bridges: A:R.232, A:R.236, A:K.239 SO4.7: 3 residues within 4Å: Chain A: I.164, K.168 Chain B: R.163 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Water bridges: B:R.163, B:R.163 Salt bridges: B:R.163, A:K.168 SO4.8: 5 residues within 4Å: Chain A: R.318, P.320, W.321, H.322, I.339 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:W.321, A:H.322 Salt bridges: A:R.318, A:H.322 SO4.9: 5 residues within 4Å: Chain A: R.270, K.319, R.323 Chain B: N.326, D.327 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Salt bridges: A:R.270, A:K.319, A:R.323 Hydrogen bonds: B:D.327 SO4.14: 4 residues within 4Å: Chain B: R.83, R.196, L.219, N.230 8 PLIP interactions: 8 interactions with chain B Water bridges: B:K.80, B:R.83, B:R.196, B:R.196, B:E.221 Salt bridges: B:K.80, B:R.83, B:R.196 SO4.15: 5 residues within 4Å: Chain A: N.326, D.327 Chain B: R.270, K.319, R.323 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Salt bridges: B:R.270, B:R.323 Hydrogen bonds: A:D.327, A:D.327, A:D.327 SO4.16: 3 residues within 4Å: Chain A: R.163 Chain B: I.164, K.168 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Water bridges: B:K.168, A:R.163, A:R.163 Salt bridges: B:K.168, A:R.163 SO4.17: 5 residues within 4Å: Chain B: R.318, P.320, W.321, H.322, I.339 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:W.321, B:H.322 Water bridges: B:R.318 Salt bridges: B:R.318, B:H.322 SO4.18: 3 residues within 4Å: Chain B: R.232, R.236, N.279 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:N.279 Water bridges: B:R.232, B:R.232, B:N.279, B:N.279 Salt bridges: B:R.232, B:R.236, B:K.239

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, H. et al., The multiple nucleotide-divalent cation binding modes of Saccharomyces cerevisiae CK2 alpha indicate a possible co-substrate hydrolysis product (ADP/GDP) release pathway. Acta Crystallogr.,Sect.D (2014)

Release Date

2014-03-05

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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