SMTL ID : 3h30.3 (2 other biounits)

Crystal structure of the catalytic subunit of human protein kinase CK2 with 5,6-dichloro-1-beta-D-ribofuranosylbenzimidazole

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.56 Å

Oligo State

homo-dimer

Ligands

3 x RFZ: 5,6-dichloro-1-beta-D-ribofuranosyl-1H-benzimidazole(Non-covalent)

RFZ.1: 8 residues within 4Å: Chain A: L.45, G.46, V.53, V.66, V.116, N.118, M.163, I.174 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:V.53, A:V.53, A:I.174 Hydrogen bonds: A:N.118 Water bridges: A:Q.123 Halogen bonds: A:V.116 RFZ.2: 9 residues within 4Å: Chain A: Y.39, Q.40, L.41, V.67, I.69, V.101, D.103, P.104, A.110 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:I.69 Hydrogen bonds: A:Q.40, A:L.41, A:D.103 RFZ.17: 12 residues within 4Å: Chain B: L.45, G.46, R.47, G.48, V.53, V.66, I.95, V.116, N.117, N.118, D.120, I.174 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:V.53, B:I.174 Water bridges: B:R.47 Halogen bonds: B:V.116

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

CL.3: 3 residues within 4Å: Chain A: V.11, H.148, A.315 Ligand excluded by PLIP CL.4: 3 residues within 4Å: Chain A: K.68, I.174, D.175 Ligand excluded by PLIP CL.5: 3 residues within 4Å: Chain A: K.158, P.159, H.160 Ligand excluded by PLIP CL.6: 5 residues within 4Å: Chain A: K.77, R.80, R.155, N.189 Ligands: CL.7 Ligand excluded by PLIP CL.7: 5 residues within 4Å: Chain A: R.155, E.180, Y.188, N.189 Ligands: CL.6 Ligand excluded by PLIP CL.8: 1 residues within 4Å: Chain A: W.24 Ligand excluded by PLIP CL.9: 4 residues within 4Å: Chain A: H.29, V.31, E.32, E.86 Ligand excluded by PLIP CL.10: 5 residues within 4Å: Chain A: K.229, F.232, F.233, H.234, R.244 Ligand excluded by PLIP CL.11: 3 residues within 4Å: Chain A: V.293, S.294, P.295 Ligand excluded by PLIP CL.12: 2 residues within 4Å: Chain A: K.198, N.238 Ligand excluded by PLIP CL.13: 3 residues within 4Å: Chain A: K.303, L.313, H.321 Ligand excluded by PLIP CL.14: 2 residues within 4Å: Chain A: R.306, Y.307 Ligand excluded by PLIP CL.15: 4 residues within 4Å: Chain A: T.251, E.252, Y.255, R.275 Ligand excluded by PLIP CL.16: 4 residues within 4Å: Chain A: R.278, K.279, R.280, R.283 Ligand excluded by PLIP CL.18: 4 residues within 4Å: Chain B: V.11, H.148, T.314, A.315 Ligand excluded by PLIP CL.19: 2 residues within 4Å: Chain B: R.80, R.155 Ligand excluded by PLIP CL.20: 3 residues within 4Å: Chain B: R.155, Y.188, N.189 Ligand excluded by PLIP CL.21: 4 residues within 4Å: Chain B: K.122, K.158, P.159, H.160 Ligand excluded by PLIP CL.22: 3 residues within 4Å: Chain B: K.68, F.113, D.175 Ligand excluded by PLIP CL.23: 4 residues within 4Å: Chain A: R.19, M.150 Chain B: H.168, K.170 Ligand excluded by PLIP CL.24: 1 residues within 4Å: Chain B: W.24 Ligand excluded by PLIP CL.25: 4 residues within 4Å: Chain A: H.168, K.170 Chain B: R.19, M.150 Ligand excluded by PLIP CL.26: 5 residues within 4Å: Chain B: K.229, F.232, F.233, H.234, R.244 Ligand excluded by PLIP CL.27: 4 residues within 4Å: Chain B: E.296, D.299, H.321, P.322 Ligand excluded by PLIP CL.28: 4 residues within 4Å: Chain B: D.253, R.278, R.306, Y.307 Ligand excluded by PLIP CL.29: 1 residues within 4Å: Chain B: V.243 Ligand excluded by PLIP CL.30: 5 residues within 4Å: Chain B: H.29, V.31, E.32, I.82, E.86 Ligand excluded by PLIP CL.31: 2 residues within 4Å: Chain A: H.18 Chain B: R.333 Ligand excluded by PLIP CL.32: 4 residues within 4Å: Chain A: H.168 Chain B: R.19, P.20, Y.23 Ligand excluded by PLIP CL.33: 2 residues within 4Å: Chain B: S.194, R.195 Ligand excluded by PLIP CL.34: 2 residues within 4Å: Chain B: K.303, H.321 Ligand excluded by PLIP CL.35: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Raaf, J. et al., The CK2alpha/CK2beta Interface of Human Protein Kinase CK2 Harbors a Binding Pocket for Small Molecules. Chem.Biol. (2008)

Release Date

2009-05-12

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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