SMTL ID : 7dxq.1

Crystal Structure of Cyanobacterial Circadian Clock Protein KaiC

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-hexamer

Ligands

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

ATP.1: 20 residues within 4Å: Chain A: T.47, S.48, G.49, T.50, G.51, K.52, T.53, L.54, S.89, F.90, I.239 Chain B: F.199, K.224, L.225, R.226, G.227, T.228, S.229, H.230 Ligands: MG.3 20 PLIP interactions: 14 interactions with chain A, 6 interactions with chain B Hydrogen bonds: A:G.49, A:T.50, A:G.51, A:K.52, A:T.53, A:T.53, A:T.53, A:L.54, A:S.89, A:S.89, B:L.225, B:H.230 Water bridges: A:T.53, A:D.145, B:R.226, B:R.226 Salt bridges: A:K.52, A:K.52, B:K.224, B:R.226 ATP.2: 25 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, T.415, R.451, I.472, S.473, D.474 Chain B: T.432, K.457, M.458, R.459, S.461, W.462, H.463, K.465 Ligands: MG.4 20 PLIP interactions: 6 interactions with chain B, 14 interactions with chain A Hydrogen bonds: B:M.458, B:S.461, B:H.463, B:K.465, A:G.291, A:G.291, A:T.292, A:G.293, A:K.294, A:T.295, A:L.296, A:T.415, A:R.451, A:D.474 Salt bridges: B:K.457, B:R.459, A:K.294, A:K.294 Water bridges: A:T.295, A:D.378 ATP.5: 23 residues within 4Å: Chain B: T.47, 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 E: F.199, K.224, L.225, R.226, G.227, T.228, S.229, H.230, K.232 Ligands: MG.7 19 PLIP interactions: 14 interactions with chain B, 5 interactions with chain E Hydrogen bonds: B:T.47, B:G.49, B:G.49, B:T.50, B:G.51, B:K.52, B:T.53, B:T.53, B:L.54, B:S.89, B:S.89, E:L.225, E:H.230, E:K.232 Water bridges: B:D.241 Salt bridges: B:K.52, B:K.52, E:K.224, E:R.226 ATP.6: 23 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, T.415, R.451, I.472, S.473 Chain E: T.432, K.457, M.458, R.459, S.461, W.462, H.463, K.465 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:L.296, B:E.318, B:S.330, B:T.415, B:R.451, E:M.458, E:S.461, E:H.463 Salt bridges: B:K.294, B:K.294, E:K.457, E:R.459 ATP.9: 24 residues within 4Å: Chain C: S.48, G.49, T.50, G.51, K.52, T.53, L.54, S.89, F.90, R.218, I.239, T.240 Chain D: E.198, F.199, L.223, K.224, L.225, R.226, G.227, T.228, S.229, H.230, K.232 Ligands: MG.11 21 PLIP interactions: 14 interactions with chain C, 7 interactions with chain D Hydrogen bonds: C:T.47, C:G.49, C:G.49, C:T.50, C:G.51, C:K.52, C:T.53, C:T.53, C:L.54, C:S.89, C:S.89, C:R.218, D:L.225, D:G.227, D:H.230 Salt bridges: C:K.52, C:K.52, D:K.224, D:R.226 Water bridges: D:R.226, 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, T.415, R.451, I.472 Chain D: T.432, K.457, M.458, R.459, G.460, S.461, W.462, H.463 Ligands: MG.12 22 PLIP interactions: 8 interactions with chain D, 14 interactions with chain C Hydrogen bonds: D:M.458, D:S.461, D:H.463, 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:S.330, C:R.451 Water bridges: D:R.459, D:R.459, D:R.459, C:T.295, C:D.378 Salt bridges: D:K.457, D:R.459, C:K.294, C:K.294 ATP.13: 21 residues within 4Å: Chain A: F.199, K.224, L.225, R.226, G.227, T.228, S.229, H.230 Chain D: S.48, G.49, T.50, G.51, K.52, T.53, L.54, S.89, F.90, I.239, T.240, D.241 Ligands: MG.15 20 PLIP interactions: 6 interactions with chain A, 14 interactions with chain D Hydrogen bonds: A:L.225, A:H.230, D:G.49, D:T.50, D:G.51, D:K.52, D:T.53, D:T.53, D:L.54, D:S.89, D:E.183, D:R.218, D:D.241, D:D.241 Water bridges: A:G.227, A:G.227 Salt bridges: A:K.224, A:R.226, D:K.52, D:K.52 ATP.14: 25 residues within 4Å: Chain A: T.432, K.457, M.458, R.459, G.460, S.461, W.462, H.463 Chain D: A.289, T.290, G.291, T.292, G.293, K.294, T.295, L.296, E.318, S.330, W.331, T.415, R.451, I.472, S.473, D.474 Ligands: MG.16 22 PLIP interactions: 6 interactions with chain A, 16 interactions with chain D Hydrogen bonds: A:M.458, A:G.460, A:S.461, A:H.463, D:A.289, D:T.290, 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:E.318, D:R.451, D:R.451 Salt bridges: A:K.457, A:R.459, D:K.294, D:K.294 Water bridges: D:E.319 ATP.17: 25 residues within 4Å: Chain E: T.47, S.48, G.49, T.50, G.51, K.52, T.53, L.54, S.89, F.90, R.218, I.239, T.240, D.241 Chain F: F.199, L.223, K.224, L.225, R.226, G.227, T.228, S.229, H.230, K.232 Ligands: MG.19 23 PLIP interactions: 17 interactions with chain E, 6 interactions with chain F Hydrogen bonds: E:T.47, E:G.49, E:G.49, E:T.50, E:T.50, E:G.51, E:K.52, E:T.53, E:T.53, E:L.54, E:S.89, E:R.218, E:R.218, E:D.241, F:L.225, F:G.227, F:H.230, F:K.232 Water bridges: E:T.53 Salt bridges: E:K.52, E:K.52, F:K.224, F:R.226 ATP.18: 25 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, T.415, R.451, I.472, S.473 Chain F: T.432, K.457, M.458, R.459, G.460, S.461, W.462, H.463, K.465 Ligands: MG.20 20 PLIP interactions: 7 interactions with chain F, 13 interactions with chain E Hydrogen bonds: F:M.458, F:G.460, F:S.461, F:H.463, F:K.465, E:G.291, E:G.291, E:T.292, E:G.293, E:K.294, E:T.295, E:T.295, E:T.295, E:L.296, E:T.415, E:R.451 Salt bridges: F:K.457, F:R.459, E:K.294, E:K.294 ATP.21: 23 residues within 4Å: Chain C: F.199, K.224, L.225, R.226, T.228, S.229, H.230, K.232 Chain F: T.47, S.48, G.49, T.50, G.51, K.52, T.53, L.54, S.89, F.90, R.218, I.239, T.240, D.241 Ligands: MG.23 20 PLIP interactions: 6 interactions with chain C, 14 interactions with chain F Hydrogen bonds: C:L.225, C:H.230, F:T.47, F:G.49, F:T.50, F:T.50, F:G.51, F:G.51, F:K.52, F:T.53, F:L.54, F:S.89, F:S.89, F:R.218 Water bridges: C:R.226, C:R.226 Salt bridges: C:K.224, C:R.226, F:K.52, F:K.52 ATP.22: 25 residues within 4Å: Chain C: 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, T.415, R.451, I.472, S.473, D.474 Ligands: MG.24 26 PLIP interactions: 18 interactions with chain F, 8 interactions with chain C Hydrogen bonds: F:T.290, F:G.291, F:T.292, F:T.292, F:G.293, F:K.294, F:T.295, F:T.295, F:L.296, F:E.318, F:E.318, F:T.415, F:R.451, F:R.451, F:D.474, F:D.474, C:M.458, C:G.460, C:H.463, C:K.465 Salt bridges: F:K.294, F:K.294, C:K.457, C:R.459 Water bridges: C:R.459, C:R.459

12 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 5 residues within 4Å: Chain A: T.53, E.78, D.145 Chain B: R.226 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: 5 residues within 4Å: Chain A: T.295, E.318, E.319, D.378 Ligands: ATP.2 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:T.295, H2O.1 MG.7: 3 residues within 4Å: Chain B: T.53, D.145 Ligands: ATP.5 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:T.53, H2O.1, H2O.1, H2O.1 MG.8: 5 residues within 4Å: Chain B: T.295, E.318, E.319, D.378 Ligands: ATP.6 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:T.295, H2O.1, H2O.1 MG.11: 5 residues within 4Å: Chain C: T.53, E.78, D.145 Chain D: R.226 Ligands: ATP.9 3 PLIP interactions: 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:T.53, H2O.2, H2O.3 MG.12: 4 residues within 4Å: Chain C: T.295, D.378 Chain D: R.459 Ligands: ATP.10 4 PLIP interactions: 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:T.295, H2O.2, H2O.2, H2O.3 MG.15: 4 residues within 4Å: Chain A: R.226 Chain D: T.53, D.145 Ligands: ATP.13 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:T.53, D:D.145 MG.16: 5 residues within 4Å: Chain A: R.459 Chain D: T.295, E.318, E.319 Ligands: ATP.14 3 PLIP interactions: 1 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:T.295, H2O.3, H2O.3 MG.19: 5 residues within 4Å: Chain E: T.53, E.78, D.145 Chain F: R.226 Ligands: ATP.17 3 PLIP interactions: 1 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:T.53, H2O.3, H2O.3 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.3, H2O.3, H2O.3 MG.23: 4 residues within 4Å: Chain C: R.226 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.4, H2O.4 MG.24: 5 residues within 4Å: Chain F: T.295, E.318, E.319, D.378 Ligands: ATP.22 3 PLIP interactions: 1 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:T.295, H2O.4, H2O.4

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Furuike, Y. et al., Elucidation of master allostery essential for circadian clock oscillation in cyanobacteria. Sci Adv (2022)

Release Date

2022-04-27

Peptides

Circadian clock protein kinase KaiC: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
E

D
F

E
C

F
D

Circadian clock protein kinase KaiC

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