SMTL ID : 8wve.1

Crystal Structure of Cyanobacterial Circadian Clock Protein KaiC

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.73 Å

Oligo State

homo-hexamer

Ligands

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

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

12 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 3 residues within 4Å: Chain A: T.53, D.145 Ligands: ATP.1 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:T.53, A:D.145, H2O.1, H2O.1, H2O.1 MG.4: 4 residues within 4Å: Chain A: T.295, E.319, D.378 Ligands: ATP.2 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:T.295, 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: 3 residues within 4Å: Chain B: T.295, 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 5 PLIP interactions: 2 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:T.53, C:D.145, H2O.2, H2O.2, H2O.2 MG.12: 4 residues within 4Å: Chain C: T.295, E.319, D.378 Ligands: ATP.10 3 PLIP interactions: 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:T.295, H2O.2, H2O.2 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.2, H2O.3 MG.16: 3 residues within 4Å: Chain D: T.295, 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 5 PLIP interactions: 2 interactions with chain E, 3 Ligand-Water interactions Metal complexes: E:T.53, E:D.145, H2O.3, H2O.3, H2O.3 MG.20: 4 residues within 4Å: Chain E: T.295, E.319, D.378 Ligands: ATP.18 3 PLIP interactions: 1 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:T.295, H2O.3, H2O.3 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.4, H2O.4 MG.24: 3 residues within 4Å: Chain F: T.295, E.319 Ligands: ATP.22 4 PLIP interactions: 1 interactions with chain F, 3 Ligand-Water interactions Metal complexes: F:T.295, H2O.3, H2O.3, H2O.3

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Furuike, Y. et al., Structure-function relationship of KaiC around dawn. Biophys Physicobio. (2024)

Release Date

2023-12-27

Peptides

Circadian clock oscillator protein KaiC: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

E
A

F
B

Circadian clock oscillator protein KaiC