SMTL ID : 7v3x.3 (3 other biounits)

Crystal Structure of Cyanobacterial Circadian Clock Protein KaiC

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.10 Å

Oligo State

homo-hexamer

Ligands

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

ATP.1: 21 residues within 4Å: Chain A: T.290, G.291, T.292, G.293, K.294, T.295, E.318, S.330, W.331, R.451, I.472 Chain B: F.456, K.457, M.458, R.459, G.460, S.461, W.462, H.463, K.465 Ligands: MG.3 20 PLIP interactions: 13 interactions with chain A, 7 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:R.451, A:R.451, B:M.458, B:G.460, B:G.460, B:H.463 Water bridges: A:E.318, B:R.459 Salt bridges: A:K.294, A:K.294, B:K.457, B:R.459 ATP.2: 21 residues within 4Å: Chain A: T.47, S.48, G.49, T.50, G.51, K.52, T.53, E.77, S.89, I.239, T.240, D.241 Chain B: F.199, L.223, K.224, R.226, T.228, S.229, H.230, K.232 Ligands: MG.4 14 PLIP interactions: 7 interactions with chain B, 7 interactions with chain A Hydrogen bonds: B:F.199, B:L.223, B:T.228, B:H.230, B:K.232, A:G.49, A:T.50, A:G.51, A:K.52, A:T.53 Salt bridges: B:K.224, B:R.226, A:K.52, A:K.52 ATP.5: 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: T.432, K.457, M.458, R.459, G.460, S.461, W.462, H.463, K.465 Ligands: MG.7 21 PLIP interactions: 13 interactions with chain B, 8 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:S.330, B:R.451, E:M.458, E:G.460, E:H.463, E:K.465 Water bridges: B:K.294, B:K.294, E:R.459, E:R.459 Salt bridges: B:K.294, B:K.294, E:K.457, E:R.459 ATP.6: 18 residues within 4Å: Chain B: S.48, G.49, T.50, G.51, K.52, T.53, L.54, S.89, F.90, I.239, T.240 Chain E: F.199, K.224, R.226, G.227, T.228, S.229, H.230 14 PLIP interactions: 9 interactions with chain B, 5 interactions with chain E Hydrogen bonds: B:G.49, B:G.49, B:G.51, B:K.52, B:T.53, B:T.53, B:L.54, E:F.199, E:G.227, E:H.230 Salt bridges: B:K.52, B:K.52, E:K.224, E:R.226 ATP.8: 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, D.474 Chain D: T.432, K.457, M.458, R.459, G.460, S.461, H.463, K.465 Ligands: MG.10 18 PLIP interactions: 13 interactions with chain C, 5 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:L.296, C:T.415, C:R.451, C:D.474, C:D.474, D:M.458, D:H.463, D:K.465 Salt bridges: C:K.294, C:K.294, D:K.457, D:R.459 ATP.9: 21 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, K.224, L.225, R.226, G.227, T.228, S.229, H.230 Ligands: MG.11 16 PLIP interactions: 12 interactions with chain C, 4 interactions with chain D Hydrogen bonds: C:G.49, C:G.49, C:T.50, C:G.51, C:K.52, C:T.53, C:L.54, C:S.89, C:D.241, C:D.241, D:L.225, D:L.225 Salt bridges: C:K.52, C:K.52, D:K.224, D:R.226 ATP.12: 23 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, T.415, R.451, I.472, S.473, D.474 Ligands: MG.14 17 PLIP interactions: 12 interactions with chain D, 5 interactions with chain A Hydrogen bonds: D:T.290, D:G.291, D:T.292, D:G.293, D:K.294, D:T.295, D:L.296, D:R.451, D:D.474, D:D.474, A:M.458, A:G.460, A:H.463 Salt bridges: D:K.294, D:K.294, A:K.457, A:R.459 ATP.13: 17 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, S.89, F.90, I.239 16 PLIP interactions: 9 interactions with chain D, 7 interactions with chain A Hydrogen bonds: D:G.49, D:T.50, D:G.51, D:K.52, D:T.53, D:T.53, D:L.54, A:F.199, A:L.225, A:G.227, A:H.230 Salt bridges: D:K.52, D:K.52, A:K.224, A:K.224, A:R.226 ATP.15: 24 residues within 4Å: Chain E: T.290, G.291, T.292, G.293, K.294, T.295, L.296, E.318, W.331, T.415, R.451, I.472, S.473, D.474 Chain F: T.432, K.457, M.458, R.459, G.460, S.461, W.462, H.463, K.465 Ligands: MG.17 24 PLIP interactions: 17 interactions with chain E, 7 interactions with chain F Hydrogen bonds: E:G.291, 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:T.415, E:R.451, E:R.451, E:D.474, F:M.458, F:H.463, F:K.465 Water bridges: E:K.294, E:T.295, F:R.459, F:R.459 Salt bridges: E:K.294, E:K.294, F:K.457, F:R.459 ATP.16: 23 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, K.224, L.225, R.226, G.227, T.228, S.229, H.230 Ligands: MG.18 22 PLIP interactions: 14 interactions with chain E, 8 interactions with chain F Hydrogen bonds: E:T.47, E:G.49, E:G.49, E:T.50, E:G.51, E:K.52, E:T.53, E:T.53, E:L.54, E:R.218, E:R.218, E:D.241, F:E.198, F:L.225, F:H.230 Salt bridges: E:K.52, E:K.52, F:K.224, F:K.224, F:R.226 Water bridges: F:G.227, F:G.227 ATP.20: 22 residues within 4Å: Chain C: F.199, K.224, L.225, R.226, G.227, 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, I.239, T.240, D.241 Ligands: MG.21 19 PLIP interactions: 13 interactions with chain F, 6 interactions with chain C Hydrogen bonds: F:G.49, 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, C:L.225, C:G.227, C:H.230 Salt bridges: F:K.52, F:K.52, C:K.224, C:K.224, C:R.226

9 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: T.295, E.318, D.378 Ligands: ATP.1 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:T.295, A:E.318, H2O.1, H2O.1 MG.4: 4 residues within 4Å: Chain A: T.53, E.77, D.145 Ligands: ATP.2 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.53 MG.7: 3 residues within 4Å: Chain B: T.295, E.318 Ligands: ATP.5 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:T.295, H2O.1, H2O.1 MG.10: 5 residues within 4Å: Chain C: T.295, E.318, E.319, D.378 Ligands: ATP.8 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:T.295, C:E.318 MG.11: 4 residues within 4Å: Chain C: T.53, D.145 Chain D: R.226 Ligands: ATP.9 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.53 MG.14: 3 residues within 4Å: Chain D: T.295, D.378 Ligands: ATP.12 No protein-ligand interaction detected (PLIP) MG.17: 5 residues within 4Å: Chain E: T.295, E.318, E.319 Chain F: R.459 Ligands: ATP.15 4 PLIP interactions: 2 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:T.295, E:E.318, H2O.1, H2O.1 MG.18: 3 residues within 4Å: Chain E: T.53 Chain F: R.226 Ligands: ATP.16 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:T.53 MG.21: 4 residues within 4Å: Chain C: R.226 Chain F: T.53, E.78 Ligands: ATP.20 3 PLIP interactions: 1 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:T.53, H2O.1, H2O.1

1 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.19: 19 residues within 4Å: Chain C: K.457, M.458, G.460, S.461, W.462, H.463 Chain F: A.289, G.291, T.292, G.293, K.294, T.295, L.296, S.330, W.331, R.451, I.472, S.473, D.474 14 PLIP interactions: 5 interactions with chain C, 9 interactions with chain F Hydrogen bonds: C:M.458, C:G.460, C:G.460, C:H.463, C:K.465, 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:R.451

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
N

B
O

C
R

D
M

E
P

F
Q

Circadian clock protein kinase KaiC

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