SMTL ID : 3k0e.1

Crystal structure of the phosphorylation-site mutant T426N of the KaiC circadian clock protein

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.20 Å

Oligo State

homo-hexamer

Ligands

20 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 6 residues within 4Å: Chain A: T.295, E.318, E.319, D.378 Ligands: MG.2, ATP.4 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.295 MG.2: 5 residues within 4Å: Chain A: T.290, G.291, T.415 Ligands: MG.1, ATP.4 No protein-ligand interaction detected (PLIP) MG.3: 3 residues within 4Å: Chain A: T.53, E.77 Ligands: ATP.5 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:T.53, A:E.77 MG.6: 8 residues within 4Å: Chain A: F.199, K.224, R.226 Chain F: S.48, G.49, K.52 Ligands: MG.30, ATP.32 No protein-ligand interaction detected (PLIP) MG.7: 5 residues within 4Å: Chain A: S.48, G.49 Chain B: F.199, K.224 Ligands: ATP.5 No protein-ligand interaction detected (PLIP) MG.8: 4 residues within 4Å: Chain B: K.294, E.318 Ligands: MG.9, ATP.11 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.318, H2O.1 MG.9: 6 residues within 4Å: Chain B: T.295, E.318, E.319 Chain C: R.459 Ligands: MG.8, ATP.11 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:T.295, H2O.1 MG.10: 4 residues within 4Å: Chain B: T.53, E.78, D.145 Ligands: ATP.12 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.53 MG.13: 5 residues within 4Å: Chain C: T.295, E.318 Chain D: R.459 Ligands: MG.14, ATP.16 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.295 MG.14: 4 residues within 4Å: Chain C: T.290, G.291 Ligands: MG.13, ATP.16 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.290 MG.15: 5 residues within 4Å: Chain C: T.53, E.78 Chain D: R.226 Ligands: ATP.17, MG.18 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.53 MG.18: 5 residues within 4Å: Chain C: T.53, D.145, S.146 Ligands: MG.15, ATP.17 No protein-ligand interaction detected (PLIP) MG.19: 5 residues within 4Å: Chain D: T.295, E.319 Chain E: R.459 Ligands: MG.20, ATP.22 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.295 MG.20: 4 residues within 4Å: Chain D: K.294, T.415 Ligands: MG.19, ATP.22 No protein-ligand interaction detected (PLIP) MG.21: 3 residues within 4Å: Chain D: T.53, E.78 Ligands: ATP.23 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.53 MG.24: 4 residues within 4Å: Chain E: T.295, E.318, E.319 Ligands: ATP.26 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:T.295 MG.25: 5 residues within 4Å: Chain E: K.52, T.53, D.145, T.181 Ligands: ATP.27 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:T.53 MG.28: 4 residues within 4Å: Chain F: T.295, E.318, E.319 Ligands: ATP.31 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:T.295 MG.29: 5 residues within 4Å: Chain E: S.48 Chain F: F.199, K.224, R.226 Ligands: ATP.27 No protein-ligand interaction detected (PLIP) MG.30: 5 residues within 4Å: Chain F: K.52, T.53, D.145 Ligands: MG.6, ATP.32 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:T.53

12 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.4: 23 residues within 4Å: Chain A: T.290, G.291, T.292, G.293, K.294, T.295, L.296, E.318, E.319, W.331, R.451, I.472, S.473 Chain B: K.457, M.458, R.459, G.460, S.461, W.462, H.463, K.465 Ligands: MG.1, MG.2 17 PLIP interactions: 6 interactions with chain B, 11 interactions with chain A Hydrogen bonds: B:M.458, B:G.460, B:H.463, B:K.465, A:G.291, A:G.293, A:K.294, A:T.295, A:T.295, A:T.295, A:L.296, A:Y.442, A:R.451, A:R.451 Salt bridges: B:K.457, B:R.459, A:K.294 ATP.5: 24 residues within 4Å: Chain A: G.49, T.50, G.51, K.52, T.53, L.54, E.77, E.78, S.89, F.90, R.218, I.239, T.240, D.241 Chain B: L.223, K.224, L.225, R.226, T.228, S.229, H.230, K.232 Ligands: MG.3, MG.7 19 PLIP interactions: 6 interactions with chain B, 13 interactions with chain A Hydrogen bonds: B:L.225, B:H.230, B:K.232, A:G.49, A:T.50, A:G.51, A:K.52, A:T.53, A:T.53, A:L.54, A:R.218, A:R.218, A:D.241, A:D.241 Water bridges: B:G.227 Salt bridges: B:K.224, B:R.226, A:K.52, A:K.52 ATP.11: 21 residues within 4Å: Chain B: T.290, G.291, T.292, G.293, K.294, T.295, L.296, W.331, R.451, I.472, D.474 Chain C: F.456, K.457, M.458, R.459, S.461, W.462, H.463, K.465 Ligands: MG.8, MG.9 19 PLIP interactions: 5 interactions with chain C, 14 interactions with chain B Hydrogen bonds: C:M.458, C:H.463, C:K.465, B:T.290, B:G.291, B:T.292, B:T.292, B:T.292, B:G.293, B:T.295, B:L.296, B:R.451, B:R.451, B:D.474, B:D.474 Salt bridges: C:K.457, C:R.459, B:K.294, B:K.294 ATP.12: 21 residues within 4Å: Chain B: G.49, T.50, G.51, K.52, T.53, L.54, E.78, S.89, F.90, R.218, I.239, T.240, D.241 Chain C: K.224, L.225, R.226, T.228, S.229, H.230, K.232 Ligands: MG.10 17 PLIP interactions: 6 interactions with chain C, 11 interactions with chain B Hydrogen bonds: C:L.225, C:H.230, C:K.232, B:G.49, B:G.51, B:T.53, B:T.53, B:L.54, B:S.89, B:R.218, B:D.241, B:D.241 Salt bridges: C:K.224, C:K.224, C:R.226, B:K.52, B:K.52 ATP.16: 25 residues within 4Å: Chain C: T.290, G.291, T.292, G.293, K.294, T.295, L.296, E.318, S.330, W.331, R.451, I.472, S.473, D.474 Chain D: T.432, K.457, M.458, R.459, G.460, S.461, W.462, H.463, K.465 Ligands: MG.13, MG.14 17 PLIP interactions: 13 interactions with chain C, 4 interactions with chain D Hydrogen bonds: C:T.290, C:G.291, C:G.291, C:G.293, C:T.295, C:T.295, C:L.296, C:R.451, C:R.451, C:D.474, D:H.463, D:K.465 Salt bridges: C:K.294, C:K.294, D:K.457, D:R.459 pi-Stacking: C:W.331 ATP.17: 23 residues within 4Å: Chain C: S.48, G.49, T.50, G.51, K.52, T.53, L.54, S.89, F.90, I.239, T.240, D.241 Chain D: F.199, L.223, K.224, L.225, R.226, G.227, T.228, H.230, K.232 Ligands: MG.15, MG.18 19 PLIP interactions: 12 interactions with chain C, 7 interactions with chain D Hydrogen bonds: C:G.49, C:G.49, C:T.50, C:G.51, C:T.53, C:T.53, C:L.54, C:S.89, C:S.89, C:D.241, D:L.225, D:T.228, D:H.230, D:K.232 Salt bridges: C:K.52, C:K.52, D:K.224, D:K.224, D:R.226 ATP.22: 25 residues within 4Å: Chain D: T.290, G.291, T.292, G.293, K.294, T.295, L.296, E.318, S.330, W.331, Y.442, R.451, I.472, S.473, D.474 Chain E: K.457, M.458, R.459, G.460, S.461, W.462, H.463, K.465 Ligands: MG.19, MG.20 18 PLIP interactions: 4 interactions with chain E, 14 interactions with chain D Hydrogen bonds: E:M.458, E:H.463, D:T.290, D:G.291, D:G.293, D:K.294, D:T.295, D:T.295, D:L.296, D:S.330, D:Y.442, D:R.451, D:R.451, D:D.474 Salt bridges: E:K.457, E:R.459, D:K.294, D:K.294 ATP.23: 22 residues within 4Å: Chain D: S.48, G.49, T.50, G.51, K.52, T.53, L.54, S.89, F.90, I.239, D.241 Chain E: F.199, L.223, K.224, L.225, R.226, G.227, T.228, S.229, H.230, K.232 Ligands: MG.21 17 PLIP interactions: 5 interactions with chain E, 12 interactions with chain D Hydrogen bonds: E:L.225, E:H.230, E:K.232, D:G.49, D:T.50, D:T.50, D:G.51, D:K.52, D:T.53, D:L.54, D:S.89, D:D.241, D:D.241 Salt bridges: E:K.224, E:R.226, D:K.52, D:K.52 ATP.26: 22 residues within 4Å: Chain E: T.290, G.291, T.292, G.293, K.294, T.295, L.296, E.318, E.319, S.330, W.331, R.451, I.472, S.473, D.474 Chain F: K.457, M.458, R.459, S.461, W.462, H.463 Ligands: MG.24 18 PLIP interactions: 14 interactions with chain E, 4 interactions with chain F Hydrogen bonds: E:T.290, E:G.291, E:G.291, E:G.293, E:K.294, E:T.295, E:T.295, E:T.295, E:L.296, E:R.451, E:D.474, E:D.474, F:M.458, F:H.463 Salt bridges: E:K.294, E:K.294, F:K.457, F:R.459 ATP.27: 21 residues within 4Å: Chain E: G.49, T.50, G.51, K.52, T.53, L.54, E.78, S.89, F.90, R.218, I.239, T.240 Chain F: L.223, K.224, L.225, R.226, T.228, S.229, H.230 Ligands: MG.25, MG.29 18 PLIP interactions: 12 interactions with chain E, 6 interactions with chain F Hydrogen bonds: E:G.49, E:T.50, E:G.51, E:K.52, E:T.53, E:L.54, E:E.78, E:S.89, E:S.89, E:R.218, F:L.225, F:H.230, F:K.232 Salt bridges: E:K.52, E:K.52, F:K.224, F:K.224, F:R.226 ATP.31: 23 residues within 4Å: Chain A: T.432, K.457, M.458, R.459, G.460, S.461, W.462, H.463, K.465 Chain F: T.290, G.291, T.292, G.293, K.294, T.295, L.296, E.318, S.330, W.331, R.451, I.472, S.473 Ligands: MG.28 18 PLIP interactions: 12 interactions with chain F, 6 interactions with chain A Hydrogen bonds: F:G.291, F:G.291, F:G.293, F:K.294, F:T.295, F:T.295, F:T.295, F:L.296, F:R.451, F:R.451, A:M.458, A:G.460, A:H.463, A:K.465 Salt bridges: F:K.294, F:K.294, A:K.457, A:R.459 ATP.32: 25 residues within 4Å: Chain A: L.223, K.224, L.225, R.226, G.227, T.228, S.229, H.230 Chain F: T.47, G.49, T.50, G.51, K.52, T.53, L.54, E.78, S.89, F.90, D.145, R.218, I.239, T.240, D.241 Ligands: MG.6, MG.30 21 PLIP interactions: 17 interactions with chain F, 4 interactions with chain A Hydrogen bonds: F:G.49, F:G.49, F:T.50, F:G.51, F:K.52, F:T.53, F:T.53, F:T.53, F:L.54, F:E.78, F:E.78, F:S.89, F:S.89, F:R.218, F:D.241, A:H.230 Salt bridges: F:K.52, F:K.52, A:K.224, A:K.224, A:R.226

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pattanayek, R. et al., Structures of KaiC Circadian Clock Mutant Proteins: A New Phosphorylation Site at T426 and Mechanisms of Kinase, ATPase and Phosphatase. Plos One (2009)

Release Date

2010-03-31

Peptides

Circadian clock protein kinase KaiC: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Circadian clock protein kinase KaiC