SMTL ID : 7s65.1

Compressed conformation of nighttime state KaiC

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-hexamer

Ligands

12 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 2 residues within 4Å: Chain A: T.295 Ligands: ADP.2 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.295 MG.4: 5 residues within 4Å: Chain A: T.53, E.78, D.145 Chain B: R.226 Ligands: ATP.3 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.53 MG.5: 3 residues within 4Å: Chain B: T.295, E.318 Ligands: ATP.6 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:T.295, B:E.318, B:E.318 MG.8: 3 residues within 4Å: Chain B: T.53, D.145 Ligands: ATP.7 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.53 MG.9: 5 residues within 4Å: Chain C: T.295, E.318, E.319 Chain D: R.459 Ligands: ATP.10 No protein-ligand interaction detected (PLIP) 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.13: 2 residues within 4Å: Chain D: T.295 Ligands: ADP.14 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.295 MG.16: 5 residues within 4Å: Chain D: T.53, E.78, D.145 Chain E: R.226 Ligands: ATP.15 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.53 MG.17: 3 residues within 4Å: Chain E: T.295, E.318 Ligands: ATP.18 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:T.295, E:E.318, E:E.318 MG.20: 3 residues within 4Å: Chain E: T.53, D.145 Ligands: ATP.19 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:T.53 MG.21: 5 residues within 4Å: Chain A: R.459 Chain F: T.295, E.318, E.319 Ligands: ATP.22 No protein-ligand interaction detected (PLIP) 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

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

ADP.2: 14 residues within 4Å: Chain A: T.290, G.291, T.292, G.293, K.294, T.295, L.296, E.318, W.331, R.451 Chain B: R.459, G.460, S.461 Ligands: MG.1 10 PLIP interactions: 8 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:G.291, A:T.292, A:G.293, A:K.294, A:T.295, A:R.451, B:G.460, B:G.460 Salt bridges: A:K.294, A:K.294 ADP.14: 14 residues within 4Å: Chain D: T.290, G.291, T.292, G.293, K.294, T.295, L.296, E.318, W.331, R.451 Chain E: R.459, G.460, S.461 Ligands: MG.13 11 PLIP interactions: 8 interactions with chain D, 3 interactions with chain E Hydrogen bonds: D:G.291, D:T.292, D:G.293, D:K.294, D:T.295, D:R.451, E:G.460, E:G.460, E:W.462 Salt bridges: D:K.294, D:K.294

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

ATP.3: 19 residues within 4Å: Chain A: S.48, G.49, T.50, G.51, K.52, T.53, S.89, F.90, R.218, I.239, D.241 Chain B: F.199, K.224, L.225, R.226, T.228, S.229, H.230 Ligands: MG.4 17 PLIP interactions: 6 interactions with chain B, 11 interactions with chain A Hydrogen bonds: B:L.225, B:R.226, B:H.230, A:G.49, A:T.50, A:G.51, A:K.52, A:T.53, A:T.53, A:E.78, A:R.218, A:D.241 Salt bridges: B:K.224, B:K.224, B:R.226, A:K.52, A:K.52 ATP.6: 18 residues within 4Å: Chain B: T.290, G.291, T.292, G.293, K.294, T.295, L.296, E.318, W.331, R.451, I.472 Chain C: F.456, K.457, M.458, R.459, S.461, H.463 Ligands: MG.5 15 PLIP interactions: 5 interactions with chain C, 10 interactions with chain B Hydrogen bonds: C:M.458, C:G.460, C:H.463, B:G.291, B:G.291, B:G.293, B:K.294, B:T.295, B:L.296, B:S.330, B:R.451 Salt bridges: C:K.457, C:R.459, B:K.294, B:K.294 ATP.7: 20 residues within 4Å: Chain B: T.47, S.48, G.49, G.51, K.52, T.53, L.54, S.89, F.90, I.239 Chain C: F.199, L.223, K.224, L.225, R.226, G.227, T.228, S.229, H.230 Ligands: MG.8 15 PLIP interactions: 11 interactions with chain B, 4 interactions with chain C Hydrogen bonds: 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, C:L.225, C:H.230 Salt bridges: B:K.52, B:K.52, C:K.224, C:R.226 ATP.10: 22 residues within 4Å: Chain C: A.289, T.290, G.291, T.292, G.293, K.294, T.295, E.318, S.330, W.331, R.451, I.472, S.473 Chain D: E.431, A.432, K.457, M.458, R.459, S.461, W.462, H.463 Ligands: MG.9 16 PLIP interactions: 5 interactions with chain D, 11 interactions with chain C Hydrogen bonds: D:A.432, D:M.458, D:M.458, C:G.291, C:G.291, C:T.292, C:G.293, C:K.294, C:T.295, C:T.295, C:S.330, C:R.451 Salt bridges: D:K.457, D:R.459, C:K.294, C:K.294 ATP.11: 21 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 Chain D: E.198, F.199, K.224, L.225, R.226, T.228, S.229, H.230 Ligands: MG.12 15 PLIP interactions: 10 interactions with chain C, 5 interactions with chain D Hydrogen bonds: C:G.49, C:T.50, C:G.51, C:G.51, C:T.53, C:L.54, C:S.89, C:R.218, D:F.199, D:L.225, D:H.230 Salt bridges: C:K.52, C:K.52, D:K.224, D:R.226 ATP.15: 19 residues within 4Å: Chain D: S.48, G.49, T.50, G.51, K.52, T.53, S.89, F.90, R.218, I.239, D.241 Chain E: F.199, K.224, L.225, R.226, 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:T.50, D:G.51, D:K.52, D:T.53, D:T.53, D:E.78, D:R.218, D:D.241, E:L.225, E:R.226, E:H.230 Salt bridges: D:K.52, D:K.52, E:K.224, E:K.224, E:R.226 ATP.18: 18 residues within 4Å: Chain E: T.290, G.291, T.292, G.293, K.294, T.295, L.296, E.318, W.331, R.451, I.472 Chain F: F.456, K.457, M.458, R.459, S.461, H.463 Ligands: MG.17 15 PLIP interactions: 5 interactions with chain F, 10 interactions with chain E Hydrogen bonds: F:M.458, F:G.460, F:H.463, E:G.291, E:G.291, E:G.293, E:K.294, E:T.295, E:L.296, E:S.330, E:R.451 Salt bridges: F:K.457, F:R.459, E:K.294, E:K.294 ATP.19: 20 residues within 4Å: Chain E: T.47, S.48, G.49, G.51, K.52, T.53, L.54, S.89, F.90, I.239 Chain F: F.199, L.223, K.224, L.225, R.226, G.227, T.228, S.229, H.230 Ligands: MG.20 15 PLIP interactions: 11 interactions with chain E, 4 interactions with chain F Hydrogen bonds: 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, F:L.225, F:H.230 Salt bridges: E:K.52, E:K.52, F:K.224, F:R.226 ATP.22: 22 residues within 4Å: Chain A: E.431, A.432, 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, E.318, S.330, W.331, R.451, I.472, S.473 Ligands: MG.21 16 PLIP interactions: 11 interactions with chain F, 5 interactions with chain A Hydrogen bonds: F:G.291, F:G.291, F:T.292, F:G.293, F:K.294, F:T.295, F:T.295, F:S.330, F:R.451, A:A.432, A:M.458, A:M.458 Salt bridges: F:K.294, F:K.294, A:K.457, A:R.459 ATP.23: 20 residues within 4Å: Chain A: F.199, K.224, L.225, R.226, 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, R.218, I.239 Ligands: MG.24 15 PLIP interactions: 10 interactions with chain F, 5 interactions with chain A Hydrogen bonds: F:G.49, F:T.50, F:G.51, F:G.51, F:T.53, F:L.54, F:S.89, F:R.218, A:F.199, A:L.225, A:H.230 Salt bridges: F:K.52, F:K.52, A:K.224, A:R.226

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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