SMTL ID : 7s66.1

Extended conformation of nighttime state KaiC

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-hexamer

Ligands

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

ATP.1: 21 residues within 4Å: Chain A: T.290, G.291, T.292, G.293, K.294, T.295, L.296, E.318, S.330, W.331, T.415, R.451, I.472, S.473 Chain B: K.457, M.458, R.459, S.461, W.462, H.463 Ligands: MG.2 17 PLIP interactions: 12 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:T.290, A:G.291, A:T.292, A:G.293, A:K.294, A:T.295, A:L.296, A:E.318, A:S.330, A:R.451, B:M.458, B:H.463 Salt bridges: A:K.294, A:K.294, B:K.457, B:K.457, B:R.459 ATP.3: 22 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, I.239, D.241 Chain B: E.198, F.199, K.224, L.225, R.226, G.227, T.228, S.229, H.230 Ligands: MG.4 17 PLIP interactions: 11 interactions with chain A, 6 interactions with chain B Hydrogen bonds: A:G.49, A:G.49, A:T.50, A:G.51, A:K.52, A:T.53, A:L.54, A:S.89, A:S.89, B:F.199, B:L.225, B:L.225 Salt bridges: A:K.52, A:K.52, B:K.224, B:K.224, B:R.226 ATP.5: 21 residues within 4Å: Chain B: T.290, G.291, T.292, G.293, K.294, T.295, L.296, E.318, S.330, W.331, T.415, R.451, I.472, S.473 Chain C: K.457, M.458, R.459, S.461, W.462, H.463 Ligands: MG.6 17 PLIP interactions: 12 interactions with chain B, 5 interactions with chain C Hydrogen bonds: B:T.290, B:G.291, B:T.292, B:G.293, B:K.294, B:T.295, B:L.296, B:E.318, B:S.330, B:R.451, C:M.458, C:H.463 Salt bridges: B:K.294, B:K.294, C:K.457, C:K.457, C:R.459 ATP.7: 22 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, I.239, D.241 Chain C: E.198, F.199, K.224, L.225, R.226, G.227, T.228, S.229, H.230 Ligands: MG.8 17 PLIP interactions: 11 interactions with chain B, 6 interactions with chain C Hydrogen bonds: B:G.49, B:G.49, B:T.50, B:G.51, B:K.52, B:T.53, B:L.54, B:S.89, B:S.89, C:F.199, C:L.225, C:L.225 Salt bridges: B:K.52, B:K.52, C:K.224, C:K.224, C:R.226 ATP.9: 21 residues within 4Å: Chain C: T.290, G.291, T.292, G.293, K.294, T.295, L.296, E.318, S.330, W.331, T.415, R.451, I.472, S.473 Chain D: K.457, M.458, R.459, S.461, W.462, H.463 Ligands: MG.10 17 PLIP interactions: 12 interactions with chain C, 5 interactions with chain D Hydrogen bonds: C:T.290, C:G.291, C:T.292, C:G.293, C:K.294, C:T.295, C:L.296, C:E.318, C:S.330, C:R.451, D:M.458, D:H.463 Salt bridges: C:K.294, C:K.294, D:K.457, D:K.457, D:R.459 ATP.11: 22 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, I.239, D.241 Chain D: E.198, F.199, K.224, L.225, R.226, G.227, T.228, S.229, H.230 Ligands: MG.12 17 PLIP interactions: 11 interactions with chain C, 6 interactions with chain D Hydrogen bonds: C:G.49, C:G.49, C:T.50, C:G.51, C:K.52, C:T.53, C:L.54, C:S.89, C:S.89, D:F.199, D:L.225, D:L.225 Salt bridges: C:K.52, C:K.52, D:K.224, D:K.224, D:R.226 ATP.13: 21 residues within 4Å: Chain D: T.290, G.291, T.292, G.293, K.294, T.295, L.296, E.318, S.330, W.331, T.415, R.451, I.472, S.473 Chain E: K.457, M.458, R.459, S.461, W.462, H.463 Ligands: MG.14 17 PLIP interactions: 12 interactions with chain D, 5 interactions with chain E Hydrogen bonds: D:T.290, D:G.291, D:T.292, D:G.293, D:K.294, D:T.295, D:L.296, D:E.318, D:S.330, D:R.451, E:M.458, E:H.463 Salt bridges: D:K.294, D:K.294, E:K.457, E:K.457, E:R.459 ATP.15: 22 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, I.239, D.241 Chain E: E.198, F.199, K.224, L.225, R.226, G.227, T.228, S.229, H.230 Ligands: MG.16 17 PLIP interactions: 11 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:T.53, D:L.54, D:S.89, D:S.89, E:F.199, E:L.225, E:L.225 Salt bridges: D:K.52, D:K.52, E:K.224, E:K.224, E:R.226 ATP.17: 21 residues within 4Å: Chain E: T.290, G.291, T.292, G.293, K.294, T.295, L.296, E.318, S.330, W.331, T.415, R.451, I.472, S.473 Chain F: K.457, M.458, R.459, S.461, W.462, H.463 Ligands: MG.18 17 PLIP interactions: 12 interactions with chain E, 5 interactions with chain F Hydrogen bonds: E:T.290, E:G.291, E:T.292, E:G.293, E:K.294, E:T.295, E:L.296, E:E.318, E:S.330, E:R.451, F:M.458, F:H.463 Salt bridges: E:K.294, E:K.294, F:K.457, F:K.457, F:R.459 ATP.19: 22 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, I.239, D.241 Chain F: E.198, F.199, K.224, L.225, R.226, G.227, T.228, S.229, H.230 Ligands: MG.20 17 PLIP interactions: 11 interactions with chain E, 6 interactions with chain F Hydrogen bonds: E:G.49, E:G.49, E:T.50, E:G.51, E:K.52, E:T.53, E:L.54, E:S.89, E:S.89, F:F.199, F:L.225, F:L.225 Salt bridges: E:K.52, E:K.52, F:K.224, F:K.224, F:R.226 ATP.21: 21 residues within 4Å: Chain A: K.457, M.458, R.459, S.461, W.462, H.463 Chain F: T.290, G.291, T.292, G.293, K.294, T.295, L.296, E.318, S.330, W.331, T.415, R.451, I.472, S.473 Ligands: MG.22 17 PLIP interactions: 12 interactions with chain F, 5 interactions with chain A Hydrogen bonds: F:T.290, F:G.291, F:T.292, F:G.293, F:K.294, F:T.295, F:L.296, F:E.318, F:S.330, F:R.451, A:M.458, A:H.463 Salt bridges: F:K.294, F:K.294, A:K.457, A:K.457, A:R.459 ATP.23: 22 residues within 4Å: Chain A: E.198, F.199, K.224, L.225, R.226, G.227, T.228, S.229, H.230 Chain F: T.47, S.48, G.49, T.50, G.51, K.52, T.53, L.54, S.89, F.90, I.239, D.241 Ligands: MG.24 17 PLIP interactions: 6 interactions with chain A, 11 interactions with chain F Hydrogen bonds: A:F.199, A:L.225, A:L.225, F:G.49, F:G.49, F:T.50, F:G.51, F:K.52, F:T.53, F:L.54, F:S.89, F:S.89 Salt bridges: A:K.224, A:K.224, A:R.226, F:K.52, F:K.52

12 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: T.295, E.318 Ligands: ATP.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.295 MG.4: 2 residues within 4Å: Chain A: T.53 Ligands: ATP.3 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.53 MG.6: 3 residues within 4Å: Chain B: T.295, E.318 Ligands: ATP.5 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.295 MG.8: 2 residues within 4Å: Chain B: T.53 Ligands: ATP.7 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.53 MG.10: 3 residues within 4Å: Chain C: T.295, E.318 Ligands: ATP.9 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.295 MG.12: 2 residues within 4Å: Chain C: T.53 Ligands: ATP.11 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.53 MG.14: 3 residues within 4Å: Chain D: T.295, E.318 Ligands: ATP.13 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.295 MG.16: 2 residues within 4Å: Chain D: T.53 Ligands: ATP.15 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.53 MG.18: 3 residues within 4Å: Chain E: T.295, E.318 Ligands: ATP.17 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:T.295 MG.20: 2 residues within 4Å: Chain E: T.53 Ligands: ATP.19 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:T.53 MG.22: 3 residues within 4Å: Chain F: T.295, E.318 Ligands: ATP.21 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:T.295 MG.24: 2 residues within 4Å: Chain F: T.53 Ligands: ATP.23 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:T.53

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Swan, J.A. et al., Coupling of distant ATPase domains in the circadian clock protein KaiC. Nat.Struct.Mol.Biol. (2022)

Release Date

2021-09-22

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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