SMTL ID : 4tl9.1

Crystal structure of N-terminal C1 domain of KaiC

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.82 Å

Oligo State

homo-hexamer

Ligands

6 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 2 residues within 4Å: Chain A: T.53 Ligands: AGS.3 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:T.53, H2O.5, H2O.5, H2O.5 MG.4: 4 residues within 4Å: Chain B: T.53, E.78, D.145 Ligands: AGS.6 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:T.53, H2O.12, H2O.12, H2O.12 MG.7: 4 residues within 4Å: Chain C: T.53, E.78, D.145 Ligands: AGS.9 4 PLIP interactions: 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:T.53, H2O.19, H2O.19, H2O.19 MG.10: 3 residues within 4Å: Chain D: T.53, E.78 Ligands: AGS.12 4 PLIP interactions: 1 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:T.53, H2O.26, H2O.26, H2O.26 MG.13: 3 residues within 4Å: Chain E: T.53, D.145 Ligands: AGS.15 4 PLIP interactions: 1 interactions with chain E, 3 Ligand-Water interactions Metal complexes: E:T.53, H2O.32, H2O.32, H2O.32 MG.16: 3 residues within 4Å: Chain F: T.53, D.145 Ligands: AGS.18 4 PLIP interactions: 1 interactions with chain F, 3 Ligand-Water interactions Metal complexes: F:T.53, H2O.37, H2O.37, H2O.37

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

CL.2: 3 residues within 4Å: Chain A: R.218, T.238, I.239 Ligand excluded by PLIP CL.5: 3 residues within 4Å: Chain B: R.218, T.238, I.239 Ligand excluded by PLIP CL.8: 3 residues within 4Å: Chain C: R.218, T.238, I.239 Ligand excluded by PLIP CL.11: 3 residues within 4Å: Chain D: R.218, T.238, I.239 Ligand excluded by PLIP CL.14: 3 residues within 4Å: Chain E: R.218, T.238, I.239 Ligand excluded by PLIP CL.17: 4 residues within 4Å: Chain A: K.232 Chain F: R.218, T.238, I.239 Ligand excluded by PLIP

6 x AGS: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER(Non-covalent)

AGS.3: 23 residues within 4Å: Chain A: T.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: F.199, K.224, L.225, R.226, G.227, T.228, S.229, H.230, K.232 Ligands: MG.1 19 PLIP interactions: 6 interactions with chain B, 13 interactions with chain A Hydrogen bonds: B:L.225, B:R.226, B:H.230, A:G.49, A:T.50, A:G.51, A:K.52, A:T.53, A:L.54, A:S.89, A:R.218, A:D.241 Water bridges: B:H.230, B:K.232, B:K.232, A:R.218, A:D.241, A:D.241 Salt bridges: A:K.52 AGS.6: 23 residues within 4Å: Chain B: T.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, G.227, T.228, S.229, H.230, K.232 Ligands: MG.4 19 PLIP interactions: 7 interactions with chain C, 12 interactions with chain B Hydrogen bonds: C:L.225, C:R.226, C:H.230, 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 Water bridges: C:G.227, C:H.230, C:K.232, C:K.232, B:R.218 Salt bridges: B:K.52 AGS.9: 22 residues within 4Å: Chain C: T.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 Ligands: MG.7 20 PLIP interactions: 5 interactions with chain D, 15 interactions with chain C Hydrogen bonds: D:L.225, D:R.226, D:H.230, 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, C:D.241, C:D.241 Water bridges: D:S.229, D:S.229, C:R.218, C:D.241, C:D.241 Salt bridges: C:K.52 AGS.12: 23 residues within 4Å: Chain D: T.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.10 23 PLIP interactions: 15 interactions with chain D, 8 interactions with chain E Hydrogen bonds: D:T.48, 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:R.218, D:D.241, E:L.225, E:R.226, E:H.230 Water bridges: D:T.53, D:R.218, D:D.241, E:H.230, E:K.232, E:K.232, E:K.232, E:K.232 Salt bridges: D:K.52 AGS.15: 22 residues within 4Å: Chain E: T.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, T.228, S.229, H.230, K.232 Ligands: MG.13 24 PLIP interactions: 17 interactions with chain E, 7 interactions with chain F Hydrogen bonds: E:T.47, E:T.48, E:G.49, E:T.50, E:G.51, E:K.52, E:T.53, E:L.54, E:S.89, E:S.89, E:R.218, F:L.225, F:R.226, F:H.230 Water bridges: E:K.52, E:T.53, E:R.218, E:D.241, E:D.241, F:G.227, F:S.229, F:K.232, F:K.232 Salt bridges: E:K.52 AGS.18: 23 residues within 4Å: Chain A: F.199, K.224, L.225, R.226, G.227, T.228, S.229, H.230, K.232 Chain F: T.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.16 21 PLIP interactions: 7 interactions with chain A, 14 interactions with chain F Hydrogen bonds: A:L.225, A:R.226, A:H.230, F:T.48, F:G.49, F:T.50, F:G.51, F:K.52, F:T.53, F:L.54, F:S.89, F:S.89, F:R.218 Water bridges: A:G.227, A:H.230, A:K.232, A:K.232, F:T.53, F:R.218, F:D.241 Salt bridges: F:K.52

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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