SMTL ID : 7dy2.1 (1 other biounit)

Crystal Structure of Cyanobacterial Circadian Clock Protein KaiC

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.04 Å

Oligo State

homo-hexamer

Ligands

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

ADP.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, R.218, I.239, T.240 Chain B: K.224, L.225, R.226, G.227, T.228, S.229, H.230 18 PLIP interactions: 11 interactions with chain A, 7 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:R.218, B:L.225, B:G.227, B:H.230 Salt bridges: A:K.52, B:K.224, B:K.224, B:R.226, B:R.226 ADP.11: 20 residues within 4Å: Chain A: K.224, L.225, G.227, T.228, S.229, H.230 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, T.240, D.241 19 PLIP interactions: 6 interactions with chain A, 13 interactions with chain D Hydrogen bonds: A:L.225, A:G.227, A:T.228, A:H.230, D:G.49, D:G.49, D:T.50, D:T.50, D:G.51, D:K.52, D:T.53, D:T.53, D:T.53, D:L.54, D:R.218, D:R.218, D:D.241 Salt bridges: A:K.224, A:K.224 ADP.14: 20 residues within 4Å: Chain E: T.47, 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: K.224, L.225, R.226, G.227, T.228, S.229, H.230 15 PLIP interactions: 12 interactions with chain E, 3 interactions with chain F Hydrogen bonds: E:T.47, 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, E:D.241, F:L.225, F:H.230, F:K.232 ADP.17: 20 residues within 4Å: Chain C: K.224, L.225, R.226, G.227, T.228, S.229, H.230, K.232 Chain F: G.49, T.50, G.51, K.52, T.53, L.54, S.89, F.90, R.218, I.239, T.240, D.241 15 PLIP interactions: 12 interactions with chain F, 3 interactions with chain C Hydrogen bonds: F:G.49, F:G.49, F:T.50, F:G.51, F:K.52, F:T.53, F:T.53, F:L.54, F:S.89, F:R.218, F:R.218, F:D.241, C:H.230 Salt bridges: C:K.224, C:K.224 ADP.18: 19 residues within 4Å: Chain C: K.457, M.458, S.461, W.462, H.463 Chain F: A.289, T.290, G.291, T.292, G.293, K.294, T.295, L.296, S.330, W.331, R.451, I.472, S.473 Ligands: MG.19 17 PLIP interactions: 13 interactions with chain F, 4 interactions with chain C Hydrogen bonds: F:A.289, 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:S.330, F:R.451, F:R.451, C:M.458, C:G.460, C:S.461, C:H.463 Salt bridges: F:K.294

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

ATP.2: 22 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, R.451, I.472, S.473 Chain B: T.432, K.457, M.458, R.459, S.461, W.462, H.463, K.465 Ligands: MG.3 23 PLIP interactions: 14 interactions with chain A, 9 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, B:M.458, B:S.461, B:H.463, B:K.465 Water bridges: A:T.295, B:R.459, B:R.459, B:R.459 Salt bridges: A:K.294, A:K.294, B:K.457, B:R.459 ATP.4: 22 residues within 4Å: Chain B: T.290, G.291, T.292, G.293, K.294, T.295, L.296, 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.6 17 PLIP interactions: 12 interactions with chain B, 5 interactions with chain E Hydrogen bonds: B:A.289, B:G.291, 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:T.415, B:R.451, E:M.458, E:H.463, E:K.465 Salt bridges: E:K.457, E:R.459 ATP.5: 19 residues within 4Å: Chain B: S.48, G.49, T.50, G.51, K.52, T.53, L.54, S.89, R.218, I.239, T.240, D.241 Chain E: K.224, L.225, R.226, G.227, T.228, S.229, H.230 17 PLIP interactions: 5 interactions with chain E, 12 interactions with chain B Hydrogen bonds: E:L.225, E:G.227, E:H.230, 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:R.218 Salt bridges: E:K.224, E:R.226, B:K.52, B:K.52 ATP.7: 18 residues within 4Å: Chain C: S.48, G.49, T.50, G.51, K.52, T.53, L.54, F.90, R.218, I.239 Chain D: F.199, L.225, R.226, G.227, T.228, S.229, H.230 Ligands: MG.9 16 PLIP interactions: 13 interactions with chain C, 3 interactions with chain D Hydrogen bonds: C:T.47, C:G.49, C:G.49, C:T.50, C:T.50, C:G.51, C:K.52, C:T.53, C:L.54, C:R.218, C:R.218, D:L.225, D:L.225 Salt bridges: C:K.52, C:K.52, D:R.226 ATP.8: 25 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, D.474 Chain D: K.457, M.458, R.459, G.460, S.461, W.462, H.463, K.465 Ligands: MG.10 24 PLIP interactions: 17 interactions with chain C, 7 interactions with chain D Hydrogen bonds: C:T.290, C:G.291, C:T.292, C:T.292, C:G.293, C:K.294, C:T.295, C:T.295, C:T.295, C:L.296, C:R.451, C:R.451, C:D.474, C:D.474, D:M.458, D:G.460, D:S.461, D:H.463, D:K.465 Salt bridges: C:K.294, C:K.294, D:K.457, D:R.459 pi-Stacking: C:W.331 ATP.12: 21 residues within 4Å: Chain A: K.457, M.458, R.459, 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, R.451, I.472, S.473 Ligands: MG.13 19 PLIP interactions: 5 interactions with chain A, 14 interactions with chain D Hydrogen bonds: A:M.458, A:S.461, A:H.463, D:A.289, D:T.290, D:T.290, D:G.291, D:T.292, D:T.292, D:G.293, D:K.294, D:T.295, D:L.296, D:R.451, D:R.451 Salt bridges: A:K.457, A:R.459, D:K.294, D:K.294 ATP.15: 22 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: K.457, M.458, R.459, S.461, W.462, H.463, K.465 Ligands: MG.16 21 PLIP interactions: 15 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:L.296, E:E.318, E:E.318, E:S.330, E:T.415, E:R.451, E:R.451, 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

7 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: T.295, E.318, D.378 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.6: 6 residues within 4Å: Chain B: T.295, E.318, E.319, D.378 Chain E: R.459 Ligands: ATP.4 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.295 MG.9: 4 residues within 4Å: Chain C: K.52, T.53, D.145 Ligands: ATP.7 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.53 MG.10: 5 residues within 4Å: Chain C: T.295, E.318, D.378, T.413 Ligands: ATP.8 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:T.295, C:E.318, C:D.378 MG.13: 3 residues within 4Å: Chain D: T.295, E.318 Ligands: ATP.12 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.295 MG.16: 5 residues within 4Å: Chain E: K.294, T.295, E.318, D.378 Ligands: ATP.15 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:T.295 MG.19: 5 residues within 4Å: Chain C: R.459 Chain F: T.295, E.318, E.319 Ligands: ADP.18 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:T.295, F:E.319

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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