SMTL ID : 4tl7.1

Crystal structure of N-terminal C1 domain of KaiC

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.94 Å

Oligo State

homo-hexamer

Ligands

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

ATP.1: 24 residues within 4Å: Chain A: 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 B: E.198, F.199, K.224, L.225, R.226, G.227, T.228, S.229, H.230, K.232 Ligands: MG.2 28 PLIP interactions: 14 interactions with chain B, 14 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:L.54, A:S.89, A:R.218, A:D.241, A:D.241 Water bridges: B:R.226, B:R.226, B:R.226, B:G.227, B:G.227, B:K.232, B:K.232, B:K.232, B:K.232, A:E.183 Salt bridges: B:K.224, B:R.226, A:K.52, A:K.52 ATP.5: 22 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, T.240, D.241 Chain C: F.199, K.224, L.225, R.226, T.228, S.229, H.230, K.232 Ligands: MG.6 28 PLIP interactions: 18 interactions with chain B, 10 interactions with chain C Hydrogen bonds: 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:R.218, B:D.241, B:D.241, C:E.198, C:L.225, C:H.230 Water bridges: B:K.52, B:K.52, B:T.53, B:D.241, B:D.241, C:R.226, C:K.232, C:K.232, C:K.232, C:K.232 Salt bridges: B:K.52, B:K.52, C:K.224, C:R.226 ATP.9: 23 residues within 4Å: Chain C: 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 D: F.199, K.224, L.225, R.226, G.227, T.228, S.229, H.230, K.232 Ligands: MG.10 26 PLIP interactions: 15 interactions with chain C, 11 interactions with chain D Hydrogen bonds: C:G.49, C:T.50, C:G.51, C:K.52, C:T.53, C:T.53, C:L.54, C:S.89, C:R.218, C:D.241, D:E.198, D:L.225, D:H.230 Water bridges: C:T.53, C:R.218, C:D.241, D:R.226, D:H.230, D:K.232, D:K.232, D:K.232, D:K.232 Salt bridges: C:K.52, C:K.52, D:K.224, D:R.226 ATP.13: 23 residues within 4Å: Chain D: 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 E: F.199, K.224, L.225, R.226, G.227, T.228, S.229, H.230, K.232 Ligands: MG.14 28 PLIP interactions: 14 interactions with chain D, 14 interactions with chain E Hydrogen bonds: D:G.49, D:T.50, D:G.51, D:K.52, D:T.53, D:L.54, D:S.89, D:R.218, D:D.241, E:L.225, E:H.230 Water bridges: D:T.53, D:E.183, D:R.218, E:R.226, E:R.226, E:R.226, E:G.227, E:G.227, E:K.232, E:K.232, E:K.232, E:K.232, E:K.232 Salt bridges: D:K.52, D:K.52, E:K.224, E:R.226 ATP.17: 23 residues within 4Å: Chain E: 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, K.232 Ligands: MG.18 27 PLIP interactions: 15 interactions with chain E, 12 interactions with chain F Hydrogen bonds: E:G.49, E:T.50, E:G.51, E:K.52, E:T.53, E:T.53, E:L.54, E:S.89, E:R.218, E:D.241, F:L.225, F:H.230 Water bridges: E:T.53, E:D.145, E:E.183, F:R.226, F:R.226, F:R.226, F:R.226, F:G.227, F:K.232, F:K.232, F:K.232 Salt bridges: E:K.52, E:K.52, F:K.224, F:R.226 ATP.21: 22 residues within 4Å: Chain A: 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, T.240, D.241 Ligands: MG.22 27 PLIP interactions: 18 interactions with chain F, 9 interactions with chain A 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:R.218, F:D.241, F:D.241, A:L.225, A:H.230 Water bridges: F:K.52, F:K.52, F:T.53, F:T.53, F:R.218, A:R.226, A:K.232, A:K.232, A:K.232, A:K.232 Salt bridges: F:K.52, F:K.52, A:K.224, A:R.226

6 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: T.53, D.145 Ligands: ATP.1 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:T.53, H2O.4, H2O.4, H2O.4 MG.6: 2 residues within 4Å: Chain B: T.53 Ligands: ATP.5 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:T.53, H2O.9, H2O.9, H2O.9 MG.10: 3 residues within 4Å: Chain C: T.53, D.145 Ligands: ATP.9 4 PLIP interactions: 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:T.53, H2O.13, H2O.13, H2O.13 MG.14: 3 residues within 4Å: Chain D: T.53, D.145 Ligands: ATP.13 4 PLIP interactions: 1 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:T.53, H2O.19, H2O.19, H2O.19 MG.18: 3 residues within 4Å: Chain E: T.53, D.145 Ligands: ATP.17 4 PLIP interactions: 1 interactions with chain E, 3 Ligand-Water interactions Metal complexes: E:T.53, H2O.24, H2O.24, H2O.24 MG.22: 3 residues within 4Å: Chain F: T.53, D.145 Ligands: ATP.21 4 PLIP interactions: 1 interactions with chain F, 3 Ligand-Water interactions Metal complexes: F:T.53, H2O.28, H2O.28, H2O.28

6 x CL: CHLORIDE ION(Non-functional Binders)

CL.3: 3 residues within 4Å: Chain A: R.218, T.238, I.239 Ligand excluded by PLIP CL.7: 3 residues within 4Å: Chain B: R.218, T.238, I.239 Ligand excluded by PLIP CL.11: 3 residues within 4Å: Chain C: R.218, T.238, I.239 Ligand excluded by PLIP CL.15: 3 residues within 4Å: Chain D: R.218, T.238, I.239 Ligand excluded by PLIP CL.19: 3 residues within 4Å: Chain E: R.218, T.238, I.239 Ligand excluded by PLIP CL.23: 3 residues within 4Å: Chain F: R.218, T.238, I.239 Ligand excluded by PLIP

6 x SO4: SULFATE ION(Non-functional Binders)

SO4.4: 3 residues within 4Å: Chain A: E.186, E.187, Y.188 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.187, A:Y.188 SO4.8: 3 residues within 4Å: Chain B: E.186, E.187, Y.188 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.187, B:Y.188 SO4.12: 3 residues within 4Å: Chain C: E.186, E.187, Y.188 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:E.187, C:Y.188 SO4.16: 3 residues within 4Å: Chain D: E.186, E.187, Y.188 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:E.187, D:Y.188 SO4.20: 3 residues within 4Å: Chain E: E.186, E.187, Y.188 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:E.187, E:Y.188 Water bridges: E:E.186, E:E.186 SO4.24: 3 residues within 4Å: Chain F: E.186, E.187, Y.188 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:E.187, F:Y.188, F:G.189

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Abe, J. et al., Circadian rhythms. Atomic-scale origins of slowness in the cyanobacterial circadian clock. Science (2015)

Release Date

2015-07-01

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

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