SMTL ID : 7dy1.1

Crystal Structure of Cyanobacterial Circadian Clock Protein KaiC

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-hexamer

Ligands

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

ATP.1: 23 residues within 4Å: Chain A: T.48, S.49, G.50, T.51, G.52, K.53, T.54, L.55, S.90, F.91, R.219, I.240 Chain B: E.199, F.200, K.225, L.226, R.227, G.228, T.229, T.230, H.231, K.233 Ligands: MG.3 22 PLIP interactions: 8 interactions with chain B, 14 interactions with chain A Hydrogen bonds: B:E.199, B:L.226, B:G.228, B:H.231, A:G.50, A:T.51, A:T.51, A:G.52, A:K.53, A:T.54, A:L.55, A:S.90, A:S.90, A:R.219 Water bridges: B:R.227, B:R.227, A:T.54, A:R.219 Salt bridges: B:K.225, B:R.227, A:K.53, A:K.53 ATP.2: 21 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 Chain B: K.457, M.458, R.459, G.460, S.461, W.462, H.463 Ligands: MG.4 30 PLIP interactions: 10 interactions with chain B, 20 interactions with chain A Hydrogen bonds: B:M.458, B:W.462, 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:S.330, A:S.330, A:T.415, A:R.451, A:R.451 Water bridges: B:R.459, B:G.460, B:G.460, B:H.463, B:K.465, B:K.465, A:G.291, A:T.295, A:T.295, A:E.318, A:T.415 Salt bridges: B:K.457, B:R.459, A:K.294, A:K.294 ATP.5: 22 residues within 4Å: Chain B: T.48, S.49, G.50, T.51, G.52, K.53, T.54, L.55, S.90, F.91, R.219, I.240 Chain C: F.200, K.225, L.226, R.227, G.228, T.229, T.230, H.231, K.233 Ligands: MG.7 21 PLIP interactions: 8 interactions with chain C, 13 interactions with chain B Hydrogen bonds: C:E.199, C:L.226, C:G.228, C:H.231, B:G.50, B:T.51, B:G.52, B:K.53, B:T.54, B:T.54, B:L.55, B:S.90, B:S.90, B:R.219 Water bridges: C:R.227, C:R.227, B:T.54 Salt bridges: C:K.225, C:R.227, B:K.53, B:K.53 ATP.6: 21 residues within 4Å: Chain B: T.290, G.291, T.292, G.293, K.294, T.295, L.296, E.318, W.331, R.451, I.472, T.473 Chain C: T.432, K.457, M.458, R.459, G.460, S.461, W.462, H.463 Ligands: MG.8 25 PLIP interactions: 16 interactions with chain B, 9 interactions with chain C Hydrogen bonds: B:T.290, 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:R.451, B:R.451, C:M.458, C:G.460, C:W.462, C:H.463 Water bridges: B:S.330, B:T.415, B:E.474, C:R.459, C:R.459, C:R.459 Salt bridges: B:K.294, B:K.294, C:K.457, C:R.459 ATP.9: 21 residues within 4Å: Chain C: S.49, G.50, T.51, G.52, K.53, T.54, L.55, S.90, F.91, R.219, I.240 Chain D: F.200, K.225, L.226, R.227, G.228, T.229, T.230, H.231, K.233 Ligands: MG.11 23 PLIP interactions: 9 interactions with chain D, 14 interactions with chain C Hydrogen bonds: D:L.226, D:H.231, C:G.50, C:T.51, C:T.51, C:G.52, C:K.53, C:T.54, C:T.54, C:L.55, C:S.90, C:S.90, C:R.219 Water bridges: D:R.227, D:R.227, D:G.228, D:G.228, D:K.233, C:R.219 Salt bridges: D:K.225, D:R.227, C:K.53, C:K.53 ATP.10: 23 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, T.473 Chain D: T.432, K.457, M.458, R.459, G.460, S.461, W.462, H.463 Ligands: MG.12 26 PLIP interactions: 16 interactions with chain C, 10 interactions with chain D Hydrogen bonds: C:T.290, C:G.291, C:T.292, C:G.293, C:K.294, C:T.295, C:L.296, C:E.318, C:S.330, C:T.415, C:R.451, C:R.451, D:M.458, D:W.462, D:H.463 Water bridges: C:E.474, C:E.474, D:R.459, D:R.459, D:R.459, D:G.460, D:G.460 Salt bridges: C:K.294, C:K.294, D:K.457, D:R.459 ATP.13: 22 residues within 4Å: Chain D: S.49, G.50, T.51, G.52, K.53, T.54, L.55, S.90, F.91, R.219, I.240 Chain E: E.199, F.200, K.225, L.226, R.227, G.228, T.229, T.230, H.231, K.233 Ligands: MG.15 25 PLIP interactions: 13 interactions with chain D, 12 interactions with chain E Hydrogen bonds: D:G.50, D:T.51, D:T.51, D:G.52, D:K.53, D:T.54, D:T.54, D:L.55, D:S.90, D:S.90, D:R.219, E:F.200, E:L.226, E:G.228, E:H.231 Salt bridges: D:K.53, D:K.53, E:K.225, E:R.227 Water bridges: E:F.200, E:R.227, E:R.227, E:R.227, E:K.233, E:K.233 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, T.415, R.451, I.472, T.473 Chain E: T.432, K.457, M.458, R.459, G.460, S.461, W.462, H.463 Ligands: MG.16 26 PLIP interactions: 16 interactions with chain D, 10 interactions with chain E Hydrogen bonds: D:A.289, D:G.291, D:T.292, D:G.293, D:K.294, D:T.295, D:T.295, D:L.296, D:E.318, D:S.330, D:S.330, D:T.415, D:R.451, D:R.451, E:M.458, E:G.460, E:W.462, E:H.463 Salt bridges: D:K.294, D:K.294, E:K.457, E:R.459 Water bridges: E:R.459, E:R.459, E:R.459, E:K.465 ATP.17: 21 residues within 4Å: Chain E: S.49, G.50, T.51, G.52, K.53, T.54, L.55, S.90, F.91, R.219, I.240 Chain F: F.200, K.225, L.226, R.227, G.228, T.229, T.230, H.231, K.233 Ligands: MG.19 25 PLIP interactions: 15 interactions with chain E, 10 interactions with chain F Hydrogen bonds: E:G.50, E:T.51, E:T.51, E:G.52, E:K.53, E:T.54, E:L.55, E:S.90, E:S.90, E:R.219, F:E.199, F:L.226, F:G.228, F:H.231, F:K.233 Water bridges: E:T.54, E:D.146, E:R.219, F:F.200, F:R.227, F:R.227 Salt bridges: E:K.53, E:K.53, F:K.225, F:R.227 ATP.18: 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 Chain F: T.432, K.457, M.458, R.459, G.460, S.461, W.462, H.463 Ligands: MG.20 25 PLIP interactions: 16 interactions with chain E, 9 interactions with chain F Hydrogen bonds: E:A.289, E:T.290, E:G.291, E:T.292, E:G.293, E:K.294, E:T.295, E:T.295, E:L.296, E:S.330, E:S.330, E:R.451, E:R.451, F:M.458, F:G.460, F:W.462, F:H.463 Water bridges: E:E.318, F:R.459, F:R.459, F:R.459 Salt bridges: E:K.294, E:K.294, F:K.457, F:R.459 ATP.21: 22 residues within 4Å: Chain A: E.199, F.200, K.225, L.226, R.227, G.228, T.229, T.230, H.231, K.233 Chain F: S.49, G.50, T.51, G.52, K.53, T.54, L.55, S.90, F.91, R.219, I.240 Ligands: MG.23 21 PLIP interactions: 13 interactions with chain F, 8 interactions with chain A Hydrogen bonds: F:G.50, F:T.51, F:G.52, F:K.53, F:T.54, F:T.54, F:L.55, F:S.90, F:S.90, F:R.219, A:F.200, A:L.226, A:H.231, A:K.233 Water bridges: F:T.54, A:R.227, A:H.231 Salt bridges: F:K.53, F:K.53, A:K.225, A:R.227 ATP.22: 23 residues within 4Å: Chain A: T.432, K.457, M.458, R.459, G.460, S.461, W.462, H.463 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, T.473 Ligands: MG.24 28 PLIP interactions: 11 interactions with chain A, 17 interactions with chain F Hydrogen bonds: A:M.458, A:H.463, F:T.290, F:G.291, F:T.292, F:G.293, F:K.294, F:T.295, F:T.295, F:L.296, F:E.318, F:S.330, F:T.415, F:R.451, F:R.451 Water bridges: A:R.459, A:R.459, A:R.459, A:G.460, A:G.460, A:W.462, A:K.465, F:T.295, F:I.472 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.54, D.146 Ligands: ATP.1 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:T.54, H2O.1, H2O.2 MG.4: 3 residues within 4Å: Chain A: T.295, E.319 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.4 MG.7: 4 residues within 4Å: Chain B: T.54, D.146 Chain C: R.227 Ligands: ATP.5 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:T.54, H2O.7, H2O.7, H2O.8 MG.8: 3 residues within 4Å: Chain B: T.295, E.318 Ligands: ATP.6 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:T.295, H2O.7, H2O.7, H2O.8 MG.11: 2 residues within 4Å: Chain C: T.54 Ligands: ATP.9 4 PLIP interactions: 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:T.54, H2O.12, H2O.12, H2O.15 MG.12: 4 residues within 4Å: Chain C: T.295, E.318, E.319 Ligands: ATP.10 4 PLIP interactions: 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:T.295, H2O.11, H2O.12, H2O.12 MG.15: 4 residues within 4Å: Chain D: T.54, D.146 Chain E: R.227 Ligands: ATP.13 4 PLIP interactions: 1 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:T.54, H2O.17, H2O.19, H2O.21 MG.16: 2 residues within 4Å: Chain D: T.295 Ligands: ATP.14 4 PLIP interactions: 1 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:T.295, H2O.18, H2O.19, H2O.21 MG.19: 3 residues within 4Å: Chain E: T.54, D.146 Ligands: ATP.17 4 PLIP interactions: 1 interactions with chain E, 3 Ligand-Water interactions Metal complexes: E:T.54, H2O.23, H2O.24, H2O.26 MG.20: 3 residues within 4Å: Chain E: T.295, E.319 Ligands: ATP.18 4 PLIP interactions: 1 interactions with chain E, 3 Ligand-Water interactions Metal complexes: E:T.295, H2O.24, H2O.24, H2O.25 MG.23: 3 residues within 4Å: Chain F: T.54, D.146 Ligands: ATP.21 4 PLIP interactions: 1 interactions with chain F, 3 Ligand-Water interactions Metal complexes: F:T.54, H2O.28, H2O.31, H2O.32 MG.24: 3 residues within 4Å: Chain F: T.295, E.318 Ligands: ATP.22 4 PLIP interactions: 1 interactions with chain F, 3 Ligand-Water interactions Metal complexes: F:T.295, H2O.28, H2O.29, H2O.29

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Furuike, Y. et al., Regulation mechanisms of the dual ATPase in KaiC. Proc.Natl.Acad.Sci.USA (2022)

Release Date

2022-05-18

Peptides

Circadian clock protein kinase KaiC: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Circadian clock protein kinase KaiC