SMTL ID : 7s67.1

Extended conformation of daytime state KaiC

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-hexamer

Ligands

6 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Covalent)

ATP.1: 19 residues within 4Å: Chain A: S.48, G.49, T.50, G.51, K.52, T.53, L.54, S.89, F.90, R.218, I.239, D.241 Chain B: K.224, L.225, R.226, T.228, S.229, H.230 Ligands: MG.2 19 PLIP interactions: 13 interactions with chain A, 6 interactions with chain B Hydrogen bonds: A:T.47, A:G.49, A:T.50, A:G.51, A:K.52, A:T.53, A:T.53, A:L.54, A:S.89, A:R.218, A:D.241, B:L.225, B:H.230 Salt bridges: A:K.52, A:K.52, B:K.224, B:R.226, B:R.226, B:R.226 ATP.5: 20 residues within 4Å: Chain A: K.224, L.225, R.226, G.227, T.228, S.229, H.230 Chain F: S.48, G.49, T.50, G.51, K.52, T.53, L.54, S.89, F.90, R.218, I.239, D.241 Ligands: MG.6 19 PLIP interactions: 6 interactions with chain A, 13 interactions with chain F Hydrogen bonds: A:L.225, A:H.230, F:T.47, F:G.49, F:T.50, F:G.51, F:K.52, F:T.53, F:T.53, F:L.54, F:S.89, F:R.218, F:D.241 Salt bridges: A:K.224, A:R.226, A:R.226, A:R.226, F:K.52, F:K.52 ATP.7: 19 residues within 4Å: Chain B: S.48, G.49, T.50, G.51, K.52, T.53, L.54, S.89, F.90, R.218, I.239, D.241 Chain C: K.224, L.225, R.226, T.228, S.229, H.230 Ligands: MG.8 19 PLIP interactions: 13 interactions with chain B, 6 interactions with chain C Hydrogen bonds: B:T.47, B:G.49, B:T.50, B:G.51, B:K.52, B:T.53, B:T.53, B:L.54, B:S.89, B:R.218, B:D.241, C:L.225, C:H.230 Salt bridges: B:K.52, B:K.52, C:K.224, C:R.226, C:R.226, C:R.226 ATP.11: 19 residues within 4Å: Chain C: S.48, G.49, T.50, G.51, K.52, T.53, L.54, S.89, F.90, R.218, I.239, D.241 Chain D: K.224, L.225, R.226, T.228, S.229, H.230 Ligands: MG.12 19 PLIP interactions: 6 interactions with chain D, 13 interactions with chain C Hydrogen bonds: D:L.225, D:H.230, C:T.47, C:G.49, C:T.50, C:G.51, C:K.52, C:T.53, C:T.53, C:L.54, C:S.89, C:R.218, C:D.241 Salt bridges: D:K.224, D:R.226, D:R.226, D:R.226, C:K.52, C:K.52 ATP.15: 19 residues within 4Å: Chain D: S.48, G.49, T.50, G.51, K.52, T.53, L.54, S.89, F.90, R.218, I.239, D.241 Chain E: K.224, L.225, R.226, T.228, S.229, H.230 Ligands: MG.16 19 PLIP interactions: 13 interactions with chain D, 6 interactions with chain E Hydrogen bonds: D:T.47, D:G.49, D:T.50, D:G.51, D:K.52, D:T.53, D:T.53, D:L.54, D:S.89, D:R.218, D:D.241, E:L.225, E:H.230 Salt bridges: D:K.52, D:K.52, E:K.224, E:R.226, E:R.226, E:R.226 ATP.22: 20 residues within 4Å: Chain E: S.48, G.49, T.50, G.51, K.52, T.53, L.54, S.89, F.90, R.218, I.239, D.241 Chain F: K.224, L.225, R.226, G.227, T.228, S.229, H.230 Ligands: MG.19 19 PLIP interactions: 13 interactions with chain E, 6 interactions with chain F Hydrogen bonds: E:T.47, E:G.49, E:T.50, E:G.51, E:K.52, E:T.53, E:T.53, E:L.54, E:S.89, E:R.218, E:D.241, F:L.225, F:H.230 Salt bridges: E:K.52, E:K.52, F:K.224, F:R.226, F:R.226, F:R.226

12 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: T.53, E.78 Chain B: R.226 Ligands: ATP.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.53 MG.4: 3 residues within 4Å: Chain A: T.295, E.318 Ligands: ADP.3 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.295 MG.6: 4 residues within 4Å: Chain A: R.226 Chain F: T.53, E.78 Ligands: ATP.5 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:T.53 MG.8: 4 residues within 4Å: Chain B: T.53, E.78 Chain C: R.226 Ligands: ATP.7 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.53 MG.10: 3 residues within 4Å: Chain B: T.295, E.318 Ligands: ADP.9 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.295 MG.12: 4 residues within 4Å: Chain C: T.53, E.78 Chain D: R.226 Ligands: ATP.11 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.53 MG.14: 3 residues within 4Å: Chain C: T.295, E.318 Ligands: ADP.13 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.295 MG.16: 4 residues within 4Å: Chain D: T.53, E.78 Chain E: R.226 Ligands: ATP.15 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.53 MG.18: 3 residues within 4Å: Chain D: T.295, E.318 Ligands: ADP.17 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.295 MG.19: 4 residues within 4Å: Chain E: T.53, E.78 Chain F: R.226 Ligands: ATP.22 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:T.53 MG.21: 3 residues within 4Å: Chain E: T.295, E.318 Ligands: ADP.20 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:T.295 MG.24: 3 residues within 4Å: Chain F: T.295, E.318 Ligands: ADP.23 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:T.295

6 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.3: 20 residues within 4Å: Chain A: A.289, T.290, G.291, T.292, G.293, K.294, T.295, L.296, S.330, W.331, R.451, I.472, S.473 Chain B: K.457, M.458, R.459, S.461, W.462, H.463 Ligands: MG.4 15 PLIP interactions: 13 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:G.291, A:T.292, A:T.292, A:G.293, A:K.294, A:T.295, A:T.295, A:T.295, A:L.296, A:S.330, A:R.451, A:R.451, B:M.458, B:H.463 Salt bridges: A:K.294 ADP.9: 20 residues within 4Å: Chain B: A.289, T.290, G.291, T.292, G.293, K.294, T.295, L.296, S.330, W.331, R.451, I.472, S.473 Chain C: K.457, M.458, R.459, S.461, W.462, H.463 Ligands: MG.10 15 PLIP interactions: 2 interactions with chain C, 13 interactions with chain B Hydrogen bonds: C:M.458, C:H.463, B:G.291, B:T.292, B:T.292, B:G.293, B:K.294, B:T.295, B:T.295, B:T.295, B:L.296, B:S.330, B:R.451, B:R.451 Salt bridges: B:K.294 ADP.13: 20 residues within 4Å: Chain C: A.289, T.290, G.291, T.292, G.293, K.294, T.295, L.296, S.330, W.331, R.451, I.472, S.473 Chain D: K.457, M.458, R.459, S.461, W.462, H.463 Ligands: MG.14 15 PLIP interactions: 2 interactions with chain D, 13 interactions with chain C Hydrogen bonds: D:M.458, D:H.463, C:G.291, C:T.292, C:T.292, C:G.293, C:K.294, C:T.295, C:T.295, C:T.295, C:L.296, C:S.330, C:R.451, C:R.451 Salt bridges: C:K.294 ADP.17: 20 residues within 4Å: Chain D: A.289, T.290, G.291, T.292, G.293, K.294, T.295, L.296, S.330, W.331, R.451, I.472, S.473 Chain E: K.457, M.458, R.459, S.461, W.462, H.463 Ligands: MG.18 15 PLIP interactions: 13 interactions with chain D, 2 interactions with chain E Hydrogen bonds: D:G.291, D:T.292, D:T.292, D:G.293, D:K.294, D:T.295, D:T.295, D:T.295, D:L.296, D:S.330, D:R.451, D:R.451, E:M.458, E:H.463 Salt bridges: D:K.294 ADP.20: 20 residues within 4Å: Chain E: A.289, T.290, G.291, T.292, G.293, K.294, T.295, L.296, S.330, W.331, R.451, I.472, S.473 Chain F: K.457, M.458, R.459, S.461, W.462, H.463 Ligands: MG.21 15 PLIP interactions: 13 interactions with chain E, 2 interactions with chain F Hydrogen bonds: E:G.291, E:T.292, E:T.292, E:G.293, E:K.294, E:T.295, E:T.295, E:T.295, E:L.296, E:S.330, E:R.451, E:R.451, F:M.458, F:H.463 Salt bridges: E:K.294 ADP.23: 20 residues within 4Å: Chain A: K.457, M.458, R.459, S.461, W.462, H.463 Chain F: A.289, T.290, G.291, T.292, G.293, K.294, T.295, L.296, S.330, W.331, R.451, I.472, S.473 Ligands: MG.24 15 PLIP interactions: 13 interactions with chain F, 2 interactions with chain A Hydrogen bonds: F:G.291, F:T.292, F:T.292, F:G.293, F:K.294, F:T.295, F:T.295, F:T.295, F:L.296, F:S.330, F:R.451, F:R.451, A:M.458, A:H.463 Salt bridges: F:K.294

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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