SMTL ID : 8wv8.1

Crystal Structure of Cyanobacterial Circadian Clock Protein KaiC

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.93 Å

Oligo State

homo-hexamer

Ligands

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

ATP.1: 21 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 Chain B: E.198, F.199, K.224, L.225, R.226, T.228, S.229, H.230 Ligands: MG.3 18 PLIP interactions: 7 interactions with chain B, 11 interactions with chain A Hydrogen bonds: B:F.199, B:L.225, B:T.228, B:H.230, 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:R.218 Salt bridges: B:K.224, B:K.224, B:R.226, A:K.52, A:K.52 ATP.2: 24 residues within 4Å: Chain A: 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: V.432, K.457, M.458, R.459, G.460, S.461, W.462, H.463, K.465 Ligands: MG.4 17 PLIP interactions: 11 interactions with chain A, 6 interactions with chain B Hydrogen bonds: A:G.291, A:T.292, A:G.293, A:K.294, A:T.295, A:T.295, A:T.295, A:L.296, A:S.330, B:M.458, B:S.461, B:H.463, B:K.465 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 20 PLIP interactions: 8 interactions with chain E, 12 interactions with chain B Hydrogen bonds: E:F.199, E:L.225, E:T.228, E:H.230, E:K.232, 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 Salt bridges: E:K.224, E:K.224, E:R.226, B:K.52, B:K.52 ATP.6: 25 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, T.415, 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.8 22 PLIP interactions: 6 interactions with chain E, 16 interactions with chain B Hydrogen bonds: E:M.458, E:S.461, E:H.463, E:K.465, B:T.290, 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:S.330, B:T.415, B:R.451, B:R.451 Salt bridges: E:K.457, E:R.459, B:K.294, B:K.294 Water bridges: B:T.295 ATP.9: 21 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 Chain D: E.198, F.199, K.224, L.225, R.226, T.228, S.229, H.230 Ligands: MG.11 18 PLIP interactions: 11 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:R.218, D:F.199, D:L.225, D:T.228, D:H.230 Salt bridges: C:K.52, C:K.52, D:K.224, D:K.224, D:R.226 ATP.10: 24 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, T.415, R.451, I.472, S.473 Chain D: V.432, K.457, M.458, R.459, G.460, S.461, W.462, H.463, K.465 Ligands: MG.12 17 PLIP interactions: 11 interactions with chain C, 6 interactions with chain D Hydrogen bonds: C:G.291, C:T.292, C:G.293, C:K.294, C:T.295, C:T.295, C:T.295, C:L.296, C:S.330, D:M.458, D:S.461, D:H.463, D:K.465 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 20 PLIP interactions: 12 interactions with chain D, 8 interactions with chain A Hydrogen bonds: 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, A:F.199, A:L.225, A:T.228, A:H.230, A:K.232 Salt bridges: D:K.52, D:K.52, A:K.224, A:K.224, A:R.226 ATP.14: 25 residues within 4Å: Chain A: V.432, K.457, M.458, R.459, G.460, S.461, W.462, H.463, K.465 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 Ligands: MG.16 22 PLIP interactions: 6 interactions with chain A, 16 interactions with chain D Hydrogen bonds: A:M.458, A:S.461, A:H.463, A:K.465, 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:S.330, D:T.415, D:R.451, D:R.451 Salt bridges: A:K.457, A:R.459, D:K.294, D:K.294 Water bridges: D:T.295 ATP.17: 21 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 Chain F: E.198, F.199, K.224, L.225, R.226, T.228, S.229, H.230 Ligands: MG.19 18 PLIP interactions: 11 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:R.218, F:F.199, F:L.225, F:T.228, F:H.230 Salt bridges: E:K.52, E:K.52, F:K.224, F:K.224, F:R.226 ATP.18: 24 residues within 4Å: Chain E: 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: V.432, K.457, M.458, R.459, G.460, S.461, W.462, H.463, K.465 Ligands: MG.20 17 PLIP interactions: 11 interactions with chain E, 6 interactions with chain F Hydrogen bonds: 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:S.330, F:M.458, F:S.461, F:H.463, F:K.465 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 20 PLIP interactions: 12 interactions with chain F, 8 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:F.199, C:L.225, C:T.228, C:H.230, C:K.232 Salt bridges: F:K.52, F:K.52, C:K.224, C:K.224, C:R.226 ATP.22: 25 residues within 4Å: Chain C: 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, T.415, R.451, I.472, S.473 Ligands: MG.24 22 PLIP interactions: 16 interactions with chain F, 6 interactions with chain C Hydrogen bonds: F:T.290, 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:S.330, F:T.415, F:R.451, F:R.451, C:M.458, C:S.461, C:H.463, C:K.465 Water bridges: F:T.295 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 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.53 MG.4: 5 residues within 4Å: Chain A: T.295, E.318, 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 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.53 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: 3 residues within 4Å: Chain C: T.53, D.145 Ligands: ATP.9 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.53 MG.12: 5 residues within 4Å: Chain C: T.295, E.318, 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.1, H2O.1 MG.15: 3 residues within 4Å: Chain D: T.53, D.145 Ligands: ATP.13 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.53 MG.16: 5 residues within 4Å: Chain D: T.295, E.318, E.319, D.378 Ligands: ATP.14 3 PLIP interactions: 1 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:T.295, H2O.1, H2O.1 MG.19: 3 residues within 4Å: Chain E: T.53, D.145 Ligands: ATP.17 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:T.53 MG.20: 5 residues within 4Å: Chain E: T.295, E.318, 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.2, H2O.2 MG.23: 3 residues within 4Å: Chain F: T.53, D.145 Ligands: ATP.21 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:T.53 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.2, H2O.2

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Furuike, Y. et al., Structure-function relationship of KaiC around dawn. Biophys Physicobio. (2023)

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