SMTL ID : 5yz8.1

Crystal Structure of N-terminal C1 domain of KaiC

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.81 Å

Oligo State

homo-hexamer

Ligands

6 x ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER(Non-covalent)

ANP.1: 23 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: E.198, F.199, K.224, L.225, R.226, G.227, T.228, W.229, H.230 Ligands: MG.2 16 PLIP interactions: 4 interactions with chain B, 12 interactions with chain A Hydrogen bonds: B:E.198, B:L.225, B:R.226, B:H.230, A:G.49, A:T.50, A:T.50, A:G.51, A:K.52, A:K.52, A:K.52, A:T.53, A:T.53, A:L.54, A:S.89, A:R.218 ANP.5: 24 residues within 4Å: Chain B: 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 C: F.199, K.224, L.225, R.226, G.227, T.228, W.229, H.230, K.232 Ligands: MG.6 17 PLIP interactions: 14 interactions with chain B, 3 interactions with chain C Hydrogen bonds: B:G.49, B:T.50, B:T.50, B:G.51, B:K.52, B:K.52, B:K.52, B:T.53, B:L.54, B:S.89, B:S.89, B:R.218, B:D.241, C:L.225, C:R.226, C:H.230 Water bridges: B:T.53 ANP.8: 23 residues within 4Å: Chain C: 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 D: F.199, K.224, L.225, R.226, G.227, T.228, W.229, H.230, K.232 Ligands: MG.9 18 PLIP interactions: 13 interactions with chain C, 5 interactions with chain D Hydrogen bonds: C:G.49, C:G.49, C:T.50, C:G.51, C:K.52, C:K.52, C:T.53, C:T.53, C:T.53, C:L.54, C:S.89, C:S.89, C:R.218, D:E.198, D:K.224, D:L.225, D:R.226, D:H.230 ANP.11: 26 residues within 4Å: 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 Chain E: E.198, F.199, L.223, K.224, L.225, R.226, G.227, T.228, W.229, H.230, K.232 Ligands: MG.12 20 PLIP interactions: 14 interactions with chain D, 6 interactions with chain E Hydrogen bonds: D:G.49, D:G.49, D:T.50, D:G.51, D:K.52, D:K.52, D:T.53, D:L.54, D:S.89, D:S.89, D:R.218, E:F.199, E:K.224, E:L.225, E:R.226, E:H.230 Water bridges: D:T.53, D:T.53, D:D.145, E:R.226 ANP.14: 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 Chain F: F.199, K.224, L.225, R.226, G.227, T.228, W.229, H.230, K.232 Ligands: MG.15 17 PLIP interactions: 5 interactions with chain F, 12 interactions with chain E Hydrogen bonds: F:K.224, F:L.225, F:R.226, F:G.227, F:H.230, E:G.49, E:T.50, E:G.51, E:K.52, E:K.52, E:T.53, E:L.54, E:S.89, E:S.89, E:R.218 Water bridges: E:T.53, E:D.145 ANP.17: 24 residues within 4Å: Chain A: E.198, F.199, K.224, L.225, R.226, G.227, T.228, W.229, H.230, K.232 Chain F: 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 Ligands: MG.18 19 PLIP interactions: 5 interactions with chain A, 14 interactions with chain F Hydrogen bonds: A:K.224, A:L.225, A:R.226, A:H.230, A:K.232, F:G.49, F:G.49, F:T.50, F:T.50, F:G.51, F:K.52, F:K.52, F:K.52, F:T.53, F:T.53, F:L.54, F:S.89, F:S.89, F:R.218

6 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: T.53, D.145 Ligands: ANP.1 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:T.53, H2O.1, H2O.1 MG.6: 3 residues within 4Å: Chain B: T.53, D.145 Ligands: ANP.5 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:T.53, H2O.1, H2O.1 MG.9: 2 residues within 4Å: Chain C: T.53 Ligands: ANP.8 3 PLIP interactions: 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:T.53, H2O.1, H2O.1 MG.12: 3 residues within 4Å: Chain D: T.53, D.145 Ligands: ANP.11 3 PLIP interactions: 1 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:T.53, H2O.1, H2O.1 MG.15: 3 residues within 4Å: Chain E: T.53, D.145 Ligands: ANP.14 3 PLIP interactions: 1 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:T.53, H2O.2, H2O.2 MG.18: 3 residues within 4Å: Chain F: T.53, D.145 Ligands: ANP.17 3 PLIP interactions: 1 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:T.53, H2O.2, H2O.2

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

CL.3: 4 residues within 4Å: Chain A: R.218, T.238, I.239 Chain B: K.232 Ligand excluded by PLIP CL.4: 3 residues within 4Å: Chain A: K.232 Chain F: R.218, I.239 Ligand excluded by PLIP CL.7: 2 residues within 4Å: Chain B: R.218, T.238 Ligand excluded by PLIP CL.10: 2 residues within 4Å: Chain C: R.218, T.238 Ligand excluded by PLIP CL.13: 2 residues within 4Å: Chain D: R.218 Chain E: K.232 Ligand excluded by PLIP CL.16: 3 residues within 4Å: Chain E: R.218, T.238, I.239 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mukaiyama, A. et al., Conformational rearrangements of the C1 ring in KaiC measure the timing of assembly with KaiB. Sci Rep (2018)

Release Date

2019-01-30

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