SMTL ID : 7wdc.1

Crystal Structure of Cyanobacterial Circadian Clock Protein KaiC

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.84 Å

Oligo State

homo-hexamer

Ligands

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

ATP.1: 18 residues within 4Å: Chain A: S.48, G.49, T.50, G.51, K.52, T.53, L.54, S.89, R.218, I.239 Chain B: F.199, K.224, L.225, R.226, T.228, S.229, H.230 Ligands: MG.3 20 PLIP interactions: 13 interactions with chain A, 7 interactions with chain B Hydrogen bonds: A:G.49, A:T.50, A:T.50, A:G.51, A:K.52, A:T.53, A:L.54, A:S.89, A:S.89, A:R.218, B:L.225, B:T.228, B:H.230 Water bridges: A:K.52, B:R.226, B:R.226 Salt bridges: A:K.52, A:K.52, B:K.224, B:R.226 ATP.2: 23 residues within 4Å: Chain A: A.289, 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 Chain B: T.432, K.457, M.458, R.459, G.460, S.461, W.462, H.463 Ligands: MG.4 24 PLIP interactions: 16 interactions with chain A, 8 interactions with chain B Hydrogen bonds: A:T.290, A:G.291, A:T.292, A:G.293, A:K.294, A:T.295, A:T.295, A:L.296, A:E.318, A:S.330, A:R.451, A:R.451, B:T.432, B:M.458, B:S.461, B:H.463 Water bridges: A:T.295, A:E.319, B:R.459, B:R.459 Salt bridges: A:K.294, A:K.294, B:K.457, B:R.459 ATP.5: 20 residues within 4Å: Chain B: S.48, G.49, T.50, G.51, K.52, T.53, L.54, S.89, F.90, R.218, I.239 Chain E: F.199, K.224, L.225, R.226, T.228, S.229, H.230, K.232 Ligands: MG.7 19 PLIP interactions: 13 interactions with chain B, 6 interactions with chain E Hydrogen bonds: B:G.49, B:T.50, B:T.50, B:G.51, B:K.52, B:T.53, B:L.54, B:S.89, B:S.89, B:R.218, E:L.225, E:H.230, E:K.232 Water bridges: B:T.53 Salt bridges: B:K.52, B:K.52, E:K.224, E:K.224, E:R.226 ATP.6: 20 residues within 4Å: Chain B: T.290, G.291, T.292, G.293, K.294, T.295, L.296, E.318, S.330, W.331, R.451, I.472 Chain E: K.457, M.458, R.459, G.460, S.461, W.462, H.463 Ligands: MG.8 18 PLIP interactions: 13 interactions with chain B, 5 interactions with chain E Hydrogen bonds: B:G.291, B:T.292, B:G.293, B:K.294, B:T.295, B:T.295, B:T.295, B:L.296, B:R.451, B:R.451, E:M.458, E:S.461, E:H.463 Water bridges: B:E.319 Salt bridges: B:K.294, B:K.294, E:K.457, E:R.459 ATP.9: 18 residues within 4Å: Chain C: S.48, G.49, T.50, G.51, K.52, T.53, L.54, S.89, R.218, I.239 Chain D: F.199, K.224, L.225, R.226, T.228, S.229, H.230 Ligands: MG.11 20 PLIP interactions: 13 interactions with chain C, 7 interactions with chain D Hydrogen bonds: C:G.49, C:T.50, C:T.50, C:G.51, C:K.52, C:T.53, C:L.54, C:S.89, C:S.89, C:R.218, D:L.225, D:T.228, D:H.230 Water bridges: C:K.52, D:R.226, D:R.226 Salt bridges: C:K.52, C:K.52, D:K.224, D:R.226 ATP.10: 23 residues within 4Å: Chain C: A.289, 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 Chain D: T.432, K.457, M.458, R.459, G.460, S.461, W.462, H.463 Ligands: MG.12 24 PLIP interactions: 16 interactions with chain C, 8 interactions with chain D Hydrogen bonds: C:T.290, C:G.291, C:T.292, C:G.293, C:K.294, C:T.295, C:T.295, C:L.296, C:E.318, C:S.330, C:R.451, C:R.451, D:T.432, D:M.458, D:S.461, D:H.463 Water bridges: C:T.295, C:E.319, D:R.459, D:R.459 Salt bridges: C:K.294, C:K.294, D:K.457, D:R.459 ATP.13: 20 residues within 4Å: Chain A: F.199, K.224, L.225, R.226, T.228, S.229, H.230, K.232 Chain D: S.48, G.49, T.50, G.51, K.52, T.53, L.54, S.89, F.90, R.218, I.239 Ligands: MG.15 19 PLIP interactions: 6 interactions with chain A, 13 interactions with chain D Hydrogen bonds: A:L.225, A:H.230, A: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:S.89, D:R.218 Salt bridges: A:K.224, A:K.224, A:R.226, D:K.52, D:K.52 Water bridges: D:T.53 ATP.14: 20 residues within 4Å: Chain A: K.457, M.458, R.459, G.460, S.461, W.462, H.463 Chain D: T.290, G.291, T.292, G.293, K.294, T.295, L.296, E.318, S.330, W.331, R.451, I.472 Ligands: MG.16 18 PLIP interactions: 13 interactions with chain D, 5 interactions with chain A Hydrogen bonds: D:G.291, D:T.292, D:G.293, D:K.294, D:T.295, D:T.295, D:T.295, D:L.296, D:R.451, D:R.451, A:M.458, A:S.461, A:H.463 Water bridges: D:E.319 Salt bridges: D:K.294, D:K.294, A:K.457, A:R.459 ATP.17: 18 residues within 4Å: Chain E: S.48, G.49, T.50, G.51, K.52, T.53, L.54, S.89, R.218, I.239 Chain F: F.199, K.224, L.225, R.226, T.228, S.229, H.230 Ligands: MG.19 20 PLIP interactions: 13 interactions with chain E, 7 interactions with chain F Hydrogen bonds: E:G.49, E:T.50, E:T.50, E:G.51, E:K.52, E:T.53, E:L.54, E:S.89, E:S.89, E:R.218, F:L.225, F:T.228, F:H.230 Water bridges: E:K.52, F:R.226, F:R.226 Salt bridges: E:K.52, E:K.52, F:K.224, F:R.226 ATP.18: 23 residues within 4Å: Chain E: A.289, 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 Chain F: T.432, K.457, M.458, R.459, G.460, S.461, W.462, H.463 Ligands: MG.20 24 PLIP interactions: 16 interactions with chain E, 8 interactions with chain F Hydrogen bonds: E:T.290, E:G.291, E:T.292, E:G.293, E:K.294, E:T.295, E:T.295, E:L.296, E:E.318, E:S.330, E:R.451, E:R.451, F:T.432, F:M.458, F:S.461, F:H.463 Water bridges: E:T.295, E:E.319, F:R.459, F:R.459 Salt bridges: E:K.294, E:K.294, F:K.457, F:R.459 ATP.21: 20 residues within 4Å: Chain C: F.199, K.224, L.225, R.226, T.228, S.229, H.230, K.232 Chain F: S.48, G.49, T.50, G.51, K.52, T.53, L.54, S.89, F.90, R.218, I.239 Ligands: MG.23 19 PLIP interactions: 13 interactions with chain F, 6 interactions with chain C Hydrogen bonds: F:G.49, F:T.50, F:T.50, F:G.51, F:K.52, F:T.53, F:L.54, F:S.89, F:S.89, F:R.218, C:L.225, C:H.230, C:K.232 Water bridges: F:T.53 Salt bridges: F:K.52, F:K.52, C:K.224, C:K.224, C:R.226 ATP.22: 20 residues within 4Å: Chain C: K.457, M.458, R.459, G.460, S.461, W.462, H.463 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 Ligands: MG.24 18 PLIP interactions: 13 interactions with chain F, 5 interactions with chain C Hydrogen bonds: F:G.291, F:T.292, F:G.293, F:K.294, F:T.295, F:T.295, F:T.295, F:L.296, F:R.451, F:R.451, C:M.458, C:S.461, C:H.463 Water bridges: F:E.319 Salt bridges: F:K.294, F:K.294, C:K.457, C:R.459

12 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 3 residues within 4Å: Chain A: T.53, D.145 Ligands: ATP.1 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:T.53, H2O.1, H2O.1 MG.4: 4 residues within 4Å: Chain A: T.295, E.318, E.319 Ligands: ATP.2 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:T.295, H2O.1, H2O.1, H2O.1 MG.7: 3 residues within 4Å: Chain B: T.53, D.145 Ligands: ATP.5 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:T.53, H2O.1, H2O.1 MG.8: 4 residues within 4Å: Chain B: T.295, E.318, E.319 Ligands: ATP.6 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:T.295, H2O.1, H2O.1, H2O.1 MG.11: 3 residues within 4Å: Chain C: T.53, D.145 Ligands: ATP.9 3 PLIP interactions: 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:T.53, H2O.1, H2O.1 MG.12: 4 residues within 4Å: Chain C: T.295, E.318, E.319 Ligands: ATP.10 4 PLIP interactions: 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:T.295, H2O.1, H2O.1, H2O.1 MG.15: 3 residues within 4Å: Chain D: T.53, D.145 Ligands: ATP.13 3 PLIP interactions: 1 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:T.53, H2O.1, H2O.2 MG.16: 4 residues within 4Å: Chain D: T.295, E.318, E.319 Ligands: ATP.14 4 PLIP interactions: 1 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:T.295, H2O.2, H2O.2, H2O.2 MG.19: 3 residues within 4Å: Chain E: T.53, D.145 Ligands: ATP.17 3 PLIP interactions: 1 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:T.53, H2O.2, H2O.2 MG.20: 4 residues within 4Å: Chain E: T.295, E.318, E.319 Ligands: ATP.18 4 PLIP interactions: 1 interactions with chain E, 3 Ligand-Water interactions Metal complexes: E:T.295, H2O.2, H2O.2, H2O.2 MG.23: 3 residues within 4Å: Chain F: T.53, D.145 Ligands: ATP.21 3 PLIP interactions: 1 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:T.53, H2O.2, H2O.2 MG.24: 4 residues within 4Å: Chain F: T.295, E.318, E.319 Ligands: ATP.22 4 PLIP interactions: 1 interactions with chain F, 3 Ligand-Water interactions Metal complexes: F:T.295, H2O.2, H2O.2, H2O.2

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mukaiyama, A. et al., Highly sensitive tryptophan fluorescence probe for detecting rhythmic conformational changes of KaiC in the cyanobacterial circadian clock system. Biochem.J. (2022)

Release Date

2022-07-20

Peptides

Circadian clock protein kinase KaiC: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

E
A

F
B

Circadian clock protein kinase KaiC