SMTL ID : 7x1y.1

Structure of the phosphorylation-site double mutant S431A/T432A of the KaiC circadian clock protein

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-hexamer

Ligands

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

ATP.1: 16 residues within 4Å: Chain A: G.278, T.279, G.280, K.281, T.282, E.305, S.317, W.318, R.438, I.459, D.461 Chain B: M.445, G.447, S.448, H.450 Ligands: MG.3 13 PLIP interactions: 11 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:G.278, A:G.278, A:T.279, A:G.280, A:K.281, A:T.282, A:S.317, A:R.438, A:R.438, B:G.447, B:H.450 Salt bridges: A:K.281, A:K.281 ATP.2: 21 residues within 4Å: Chain A: T.34, S.35, G.36, T.37, G.38, K.39, T.40, L.41, S.76, F.77, R.205, I.226 Chain B: F.186, K.211, L.212, R.213, G.214, T.215, S.216, H.217 Ligands: MG.4 18 PLIP interactions: 12 interactions with chain A, 6 interactions with chain B Hydrogen bonds: A:G.36, A:G.36, A:T.37, A:G.38, A:K.39, A:T.40, A:L.41, A:S.76, A:S.76, A:R.205, B:L.212, B:R.213, B:H.217 Salt bridges: A:K.39, A:K.39, B:K.211, B:K.211, B:R.213 ATP.5: 18 residues within 4Å: Chain B: G.278, T.279, G.280, K.281, T.282, E.305, E.306, S.317, W.318, S.366, R.438, I.459, D.461 Chain C: M.445, G.447, S.448, H.450 Ligands: MG.7 13 PLIP interactions: 11 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:G.278, B:G.278, B:T.279, B:G.280, B:K.281, B:T.282, B:S.317, B:R.438, B:R.438, C:G.447, C:H.450 Salt bridges: B:K.281, B:K.281 ATP.6: 21 residues within 4Å: Chain B: T.34, S.35, G.36, T.37, G.38, K.39, T.40, L.41, S.76, F.77, R.205, I.226 Chain C: F.186, K.211, L.212, R.213, G.214, T.215, S.216, H.217 Ligands: MG.8 19 PLIP interactions: 13 interactions with chain B, 6 interactions with chain C Hydrogen bonds: B:G.36, B:G.36, B:T.37, B:G.38, B:K.39, B:T.40, B:L.41, B:S.76, B:S.76, B:R.205, B:R.205, C:L.212, C:R.213, C:H.217 Salt bridges: B:K.39, B:K.39, C:K.211, C:K.211, C:R.213 ATP.9: 16 residues within 4Å: Chain C: G.278, T.279, G.280, K.281, T.282, E.305, S.317, W.318, R.438, I.459 Chain D: M.445, R.446, G.447, S.448, H.450 Ligands: MG.11 15 PLIP interactions: 3 interactions with chain D, 12 interactions with chain C Hydrogen bonds: D:R.446, D:G.447, D:H.450, C:G.278, C:G.278, C:T.279, C:G.280, C:K.281, C:T.282, C:L.283, C:S.317, C:R.438, C:R.438 Salt bridges: C:K.281, C:K.281 ATP.10: 21 residues within 4Å: Chain C: T.34, S.35, G.36, T.37, G.38, K.39, T.40, L.41, S.76, F.77, R.205, I.226 Chain D: F.186, K.211, L.212, R.213, G.214, T.215, S.216, H.217 Ligands: MG.12 17 PLIP interactions: 5 interactions with chain D, 12 interactions with chain C Hydrogen bonds: D:L.212, D:H.217, C:G.36, C:G.36, C:T.37, C:G.38, C:K.39, C:T.40, C:L.41, C:S.76, C:S.76, C:R.205 Salt bridges: D:K.211, D:K.211, D:R.213, C:K.39, C:K.39 ATP.13: 18 residues within 4Å: Chain D: G.278, T.279, G.280, K.281, T.282, E.305, E.306, S.317, W.318, S.366, R.438, I.459, D.461 Chain E: M.445, G.447, S.448, H.450 Ligands: MG.15 14 PLIP interactions: 12 interactions with chain D, 2 interactions with chain E Hydrogen bonds: D:G.278, D:G.278, D:T.279, D:G.280, D:K.281, D:T.282, D:E.306, D:S.317, D:R.438, D:R.438, E:G.447, E:H.450 Salt bridges: D:K.281, D:K.281 ATP.14: 21 residues within 4Å: Chain D: T.34, S.35, G.36, T.37, G.38, K.39, T.40, L.41, S.76, F.77, R.205, I.226 Chain E: F.186, K.211, L.212, R.213, G.214, T.215, S.216, H.217 Ligands: MG.16 19 PLIP interactions: 13 interactions with chain D, 6 interactions with chain E Hydrogen bonds: D:G.36, D:G.36, D:T.37, D:G.38, D:K.39, D:T.40, D:T.40, D:L.41, D:S.76, D:S.76, D:R.205, E:L.212, E:R.213, E:H.217 Salt bridges: D:K.39, D:K.39, E:K.211, E:K.211, E:R.213 ATP.17: 18 residues within 4Å: Chain E: G.278, T.279, G.280, K.281, T.282, E.305, E.306, S.317, W.318, S.366, R.438, I.459, D.461 Chain F: M.445, G.447, S.448, H.450 Ligands: MG.19 16 PLIP interactions: 2 interactions with chain F, 14 interactions with chain E Hydrogen bonds: F:G.447, F:H.450, E:G.278, E:G.278, E:T.279, E:G.280, E:K.281, E:T.282, E:L.283, E:E.305, E:S.317, E:S.366, E:R.438, E:R.438 Salt bridges: E:K.281, E:K.281 ATP.18: 21 residues within 4Å: Chain E: T.34, S.35, G.36, T.37, G.38, K.39, T.40, L.41, S.76, F.77, R.205, I.226 Chain F: F.186, K.211, L.212, R.213, G.214, T.215, S.216, H.217 Ligands: MG.20 19 PLIP interactions: 13 interactions with chain E, 6 interactions with chain F Hydrogen bonds: E:G.36, E:G.36, E:T.37, E:G.38, E:K.39, E:T.40, E:L.41, E:S.76, E:S.76, E:R.205, E:R.205, F:L.212, F:R.213, F:H.217 Salt bridges: E:K.39, E:K.39, F:K.211, F:K.211, F:R.213 ATP.21: 17 residues within 4Å: Chain A: M.445, G.447, S.448, H.450 Chain F: G.278, T.279, G.280, K.281, T.282, E.305, E.306, S.317, W.318, S.366, R.438, I.459 Ligands: MG.23 17 PLIP interactions: 2 interactions with chain A, 15 interactions with chain F Hydrogen bonds: A:G.447, A:H.450, F:G.278, F:G.278, F:T.279, F:G.280, F:K.281, F:T.282, F:L.283, F:E.305, F:E.306, F:S.317, F:S.366, F:R.438, F:R.438 Salt bridges: F:K.281, F:K.281 ATP.22: 21 residues within 4Å: Chain A: F.186, K.211, L.212, R.213, G.214, T.215, S.216, H.217 Chain F: T.34, S.35, G.36, T.37, G.38, K.39, T.40, L.41, S.76, F.77, R.205, I.226 Ligands: MG.24 17 PLIP interactions: 5 interactions with chain A, 12 interactions with chain F Hydrogen bonds: A:L.212, A:H.217, F:G.36, F:G.36, F:T.37, F:G.38, F:K.39, F:T.40, F:L.41, F:S.76, F:S.76, F:R.205 Salt bridges: A:K.211, A:K.211, A:R.213, F:K.39, F:K.39

12 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 5 residues within 4Å: Chain A: T.282, E.305, D.365, S.366 Ligands: ATP.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.282 MG.4: 3 residues within 4Å: Chain A: T.40, E.65 Ligands: ATP.2 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.40 MG.7: 5 residues within 4Å: Chain B: T.282, E.305, D.365, S.366 Ligands: ATP.5 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.282 MG.8: 3 residues within 4Å: Chain B: T.40, E.65 Ligands: ATP.6 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.40 MG.11: 5 residues within 4Å: Chain C: T.282, E.305, D.365, S.366 Ligands: ATP.9 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:T.282, C:D.365, C:D.365 MG.12: 3 residues within 4Å: Chain C: T.40, E.65 Ligands: ATP.10 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.40 MG.15: 5 residues within 4Å: Chain D: T.282, E.305, D.365, S.366 Ligands: ATP.13 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.282 MG.16: 3 residues within 4Å: Chain D: T.40, E.65 Ligands: ATP.14 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.40 MG.19: 5 residues within 4Å: Chain E: T.282, E.305, D.365, S.366 Ligands: ATP.17 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:T.282 MG.20: 3 residues within 4Å: Chain E: T.40, E.65 Ligands: ATP.18 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:T.40 MG.23: 5 residues within 4Å: Chain F: T.282, E.305, D.365, S.366 Ligands: ATP.21 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:T.282 MG.24: 3 residues within 4Å: Chain F: T.40, E.65 Ligands: ATP.22 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:T.40

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Han, X. et al., Determining subunit-subunit interaction from statistics of cryo-EM images: observation of nearest-neighbor coupling in a circadian clock protein complex. Nat Commun (2023)

Release Date

2023-04-26

Peptides

Circadian clock oscillator protein KaiC: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Circadian clock oscillator protein KaiC