SMTL ID : 8jon.1

Structure of a synthetic circadian clock protein KaiC mutant of cyanobacteria Synechococcus elongatus PCC 7942

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-hexamer

Ligands

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

ATP.1: 25 residues within 4Å: Chain A: T.51, S.52, G.53, T.54, G.55, K.56, T.57, L.58, F.59, S.93, F.94, R.222, I.243, N.244, D.245 Chain B: F.203, L.227, K.228, L.229, R.230, G.231, T.232, T.233, H.234 Ligands: MG.2 18 PLIP interactions: 14 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:G.53, A:G.53, A:T.54, A:G.55, A:K.56, A:T.57, A:T.57, A:L.58, A:S.93, A:S.93, A:R.222, A:R.222, B:L.229, B:H.234 Salt bridges: A:K.56, A:K.56, B:K.228, B:R.230 ATP.5: 25 residues within 4Å: Chain B: T.51, S.52, G.53, T.54, G.55, K.56, T.57, L.58, F.59, S.93, F.94, R.222, I.243, N.244, D.245 Chain C: F.203, L.227, K.228, L.229, R.230, G.231, T.232, T.233, H.234 Ligands: MG.6 18 PLIP interactions: 14 interactions with chain B, 4 interactions with chain C Hydrogen bonds: B:G.53, B:G.53, B:T.54, B:G.55, B:K.56, B:T.57, B:T.57, B:L.58, B:S.93, B:S.93, B:R.222, B:R.222, C:L.229, C:H.234 Salt bridges: B:K.56, B:K.56, C:K.228, C:R.230 ATP.9: 25 residues within 4Å: Chain C: T.51, S.52, G.53, T.54, G.55, K.56, T.57, L.58, F.59, S.93, F.94, R.222, I.243, N.244, D.245 Chain D: F.203, L.227, K.228, L.229, R.230, G.231, T.232, T.233, H.234 Ligands: MG.10 18 PLIP interactions: 14 interactions with chain C, 4 interactions with chain D Hydrogen bonds: C:G.53, C:G.53, C:T.54, C:G.55, C:K.56, C:T.57, C:T.57, C:L.58, C:S.93, C:S.93, C:R.222, C:R.222, D:L.229, D:H.234 Salt bridges: C:K.56, C:K.56, D:K.228, D:R.230 ATP.13: 25 residues within 4Å: Chain D: T.51, S.52, G.53, T.54, G.55, K.56, T.57, L.58, F.59, S.93, F.94, R.222, I.243, N.244, D.245 Chain E: F.203, L.227, K.228, L.229, R.230, G.231, T.232, T.233, H.234 Ligands: MG.14 18 PLIP interactions: 4 interactions with chain E, 14 interactions with chain D Hydrogen bonds: E:L.229, E:H.234, D:G.53, D:G.53, D:T.54, D:G.55, D:K.56, D:T.57, D:T.57, D:L.58, D:S.93, D:S.93, D:R.222, D:R.222 Salt bridges: E:K.228, E:R.230, D:K.56, D:K.56 ATP.17: 25 residues within 4Å: Chain E: T.51, S.52, G.53, T.54, G.55, K.56, T.57, L.58, F.59, S.93, F.94, R.222, I.243, N.244, D.245 Chain F: F.203, L.227, K.228, L.229, R.230, G.231, T.232, T.233, H.234 Ligands: MG.18 18 PLIP interactions: 14 interactions with chain E, 4 interactions with chain F Hydrogen bonds: E:G.53, E:G.53, E:T.54, E:G.55, E:K.56, E:T.57, E:T.57, E:L.58, E:S.93, E:S.93, E:R.222, E:R.222, F:L.229, F:H.234 Salt bridges: E:K.56, E:K.56, F:K.228, F:R.230 ATP.21: 25 residues within 4Å: Chain A: F.203, L.227, K.228, L.229, R.230, G.231, T.232, T.233, H.234 Chain F: T.51, S.52, G.53, T.54, G.55, K.56, T.57, L.58, F.59, S.93, F.94, R.222, I.243, N.244, D.245 Ligands: MG.22 18 PLIP interactions: 14 interactions with chain F, 4 interactions with chain A Hydrogen bonds: F:G.53, F:G.53, F:T.54, F:G.55, F:K.56, F:T.57, F:T.57, F:L.58, F:S.93, F:S.93, F:R.222, F:R.222, A:L.229, A:H.234 Salt bridges: F:K.56, F:K.56, A:K.228, A:R.230

12 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: T.57, E.82, D.149 Chain B: R.230 Ligands: ATP.1 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:T.57, A:E.82 MG.4: 6 residues within 4Å: Chain A: T.299, E.322, E.323, S.383 Chain B: R.463 Ligands: ADP.3 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.299 MG.6: 5 residues within 4Å: Chain B: T.57, E.82, D.149 Chain C: R.230 Ligands: ATP.5 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:T.57, B:E.82 MG.8: 6 residues within 4Å: Chain B: T.299, E.322, E.323, S.383 Chain C: R.463 Ligands: ADP.7 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.299 MG.10: 5 residues within 4Å: Chain C: T.57, E.82, D.149 Chain D: R.230 Ligands: ATP.9 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:T.57, C:E.82 MG.12: 6 residues within 4Å: Chain C: T.299, E.322, E.323, S.383 Chain D: R.463 Ligands: ADP.11 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.299 MG.14: 5 residues within 4Å: Chain D: T.57, E.82, D.149 Chain E: R.230 Ligands: ATP.13 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:T.57, D:E.82 MG.16: 6 residues within 4Å: Chain D: T.299, E.322, E.323, S.383 Chain E: R.463 Ligands: ADP.15 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.299 MG.18: 5 residues within 4Å: Chain E: T.57, E.82, D.149 Chain F: R.230 Ligands: ATP.17 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:T.57, E:E.82 MG.20: 6 residues within 4Å: Chain E: T.299, E.322, E.323, S.383 Chain F: R.463 Ligands: ADP.19 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:T.299 MG.22: 5 residues within 4Å: Chain A: R.230 Chain F: T.57, E.82, D.149 Ligands: ATP.21 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:T.57, F:E.82 MG.24: 6 residues within 4Å: Chain A: R.463 Chain F: T.299, E.322, E.323, S.383 Ligands: ADP.23 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:T.299

6 x ADP: ADENOSINE-5'-DIPHOSPHATE(Covalent)

ADP.3: 24 residues within 4Å: Chain A: A.293, T.294, G.295, T.296, G.297, K.298, T.299, L.300, E.323, S.334, W.335, R.455, I.476, T.477, D.478 Chain B: K.461, M.462, R.463, G.464, S.465, W.466, H.467, K.469 Ligands: MG.4 15 PLIP interactions: 12 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:G.295, A:T.296, A:G.297, A:K.298, A:T.299, A:T.299, A:L.300, A:W.335, A:R.455, A:R.455, A:D.478, B:M.462, B:G.464, B:H.467 Salt bridges: A:K.298 ADP.7: 24 residues within 4Å: Chain B: A.293, T.294, G.295, T.296, G.297, K.298, T.299, L.300, E.323, S.334, W.335, R.455, I.476, T.477, D.478 Chain C: K.461, M.462, R.463, G.464, S.465, W.466, H.467, K.469 Ligands: MG.8 15 PLIP interactions: 3 interactions with chain C, 12 interactions with chain B Hydrogen bonds: C:M.462, C:G.464, C:H.467, B:G.295, B:T.296, B:G.297, B:K.298, B:T.299, B:T.299, B:L.300, B:W.335, B:R.455, B:R.455, B:D.478 Salt bridges: B:K.298 ADP.11: 24 residues within 4Å: Chain C: A.293, T.294, G.295, T.296, G.297, K.298, T.299, L.300, E.323, S.334, W.335, R.455, I.476, T.477, D.478 Chain D: K.461, M.462, R.463, G.464, S.465, W.466, H.467, K.469 Ligands: MG.12 15 PLIP interactions: 12 interactions with chain C, 3 interactions with chain D Hydrogen bonds: C:G.295, C:T.296, C:G.297, C:K.298, C:T.299, C:T.299, C:L.300, C:S.334, C:W.335, C:R.455, C:R.455, D:M.462, D:G.464, D:H.467 Salt bridges: C:K.298 ADP.15: 24 residues within 4Å: Chain D: A.293, T.294, G.295, T.296, G.297, K.298, T.299, L.300, E.323, S.334, W.335, R.455, I.476, T.477, D.478 Chain E: K.461, M.462, R.463, G.464, S.465, W.466, H.467, K.469 Ligands: MG.16 15 PLIP interactions: 12 interactions with chain D, 3 interactions with chain E Hydrogen bonds: D:G.295, D:T.296, D:G.297, D:K.298, D:T.299, D:T.299, D:L.300, D:W.335, D:R.455, D:R.455, D:D.478, E:M.462, E:G.464, E:H.467 Salt bridges: D:K.298 ADP.19: 24 residues within 4Å: Chain E: A.293, T.294, G.295, T.296, G.297, K.298, T.299, L.300, E.323, S.334, W.335, R.455, I.476, T.477, D.478 Chain F: K.461, M.462, R.463, G.464, S.465, W.466, H.467, K.469 Ligands: MG.20 15 PLIP interactions: 12 interactions with chain E, 3 interactions with chain F Hydrogen bonds: E:G.295, E:T.296, E:G.297, E:K.298, E:T.299, E:T.299, E:L.300, E:S.334, E:W.335, E:R.455, E:R.455, F:M.462, F:G.464, F:H.467 Salt bridges: E:K.298 ADP.23: 24 residues within 4Å: Chain A: K.461, M.462, R.463, G.464, S.465, W.466, H.467, K.469 Chain F: A.293, T.294, G.295, T.296, G.297, K.298, T.299, L.300, E.323, S.334, W.335, R.455, I.476, T.477, D.478 Ligands: MG.24 15 PLIP interactions: 12 interactions with chain F, 3 interactions with chain A Hydrogen bonds: F:G.295, F:T.296, F:G.297, F:K.298, F:T.299, F:T.299, F:L.300, F:W.335, F:R.455, F:R.455, F:D.478, A:M.462, A:G.464, A:H.467 Salt bridges: F:K.298

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, S. et al., Adaptation of ancient cyanobacterial clock to the day length ~ 0.95 Ga ago. To Be Published

Release Date

2024-06-12

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