SMTL ID : 8fwi.1

Structure of dodecameric KaiC-RS-S413E/S414E solved by cryo-EM

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-12-mer

Ligands

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

ATP.1: 24 residues within 4Å: Chain A: V.275, A.276, G.277, A.278, G.279, K.280, S.281, S.282, S.316, L.317, L.401, R.435, M.456, S.457, D.458 Chain D: E.416, K.441, A.442, R.443, G.444, M.445, A.446, H.447 Ligands: MG.3 20 PLIP interactions: 13 interactions with chain A, 7 interactions with chain D Hydrogen bonds: A:G.277, A:G.277, A:A.278, A:G.279, A:K.280, A:S.281, A:S.282, A:S.282, A:S.316, A:S.316, A:R.435, D:E.416, D:E.416, D:A.442, D:M.445, D:H.447 Salt bridges: A:K.280, A:K.280, D:K.441, D:R.443 ATP.5: 23 residues within 4Å: Chain B: V.275, A.276, G.277, A.278, G.279, K.280, S.281, S.282, S.316, L.317, R.435, M.456, S.457, D.458 Chain K: E.416, K.441, A.442, R.443, G.444, M.445, A.446, H.447 Ligands: MG.7 21 PLIP interactions: 14 interactions with chain B, 7 interactions with chain K Hydrogen bonds: B:G.277, B:G.277, B:A.278, B:G.279, B:K.280, B:S.281, B:S.281, B:S.282, B:S.282, B:S.316, B:S.316, B:R.435, K:E.416, K:E.416, K:A.442, K:M.445, K:H.447 Salt bridges: B:K.280, B:K.280, K:K.441, K:R.443 ATP.9: 24 residues within 4Å: Chain B: E.416, K.441, A.442, R.443, G.444, M.445, A.446, H.447 Chain C: V.275, A.276, G.277, A.278, G.279, K.280, S.281, S.282, S.316, L.317, L.401, R.435, M.456, S.457, D.458 Ligands: MG.11 21 PLIP interactions: 7 interactions with chain B, 14 interactions with chain C Hydrogen bonds: B:E.416, B:E.416, B:A.442, B:M.445, B:H.447, C:G.277, C:G.277, C:A.278, C:G.279, C:K.280, C:S.281, C:S.281, C:S.282, C:S.282, C:S.316, C:S.316, C:R.435 Salt bridges: B:K.441, B:R.443, C:K.280, C:K.280 ATP.13: 24 residues within 4Å: Chain D: V.275, A.276, G.277, A.278, G.279, K.280, S.281, S.282, S.316, L.317, L.401, R.435, M.456, S.457, D.458 Chain F: E.416, K.441, A.442, R.443, G.444, M.445, A.446, H.447 Ligands: MG.15 20 PLIP interactions: 13 interactions with chain D, 7 interactions with chain F Hydrogen bonds: D:G.277, D:G.277, D:A.278, D:G.279, D:K.280, D:S.281, D:S.282, D:S.282, D:S.316, D:S.316, D:R.435, F:E.416, F:E.416, F:A.442, F:M.445, F:H.447 Salt bridges: D:K.280, D:K.280, F:K.441, F:R.443 ATP.17: 24 residues within 4Å: Chain C: E.416, K.441, A.442, R.443, G.444, M.445, A.446, H.447 Chain E: V.275, A.276, G.277, A.278, G.279, K.280, S.281, S.282, S.316, L.317, L.401, R.435, M.456, S.457, D.458 Ligands: MG.19 21 PLIP interactions: 7 interactions with chain C, 14 interactions with chain E Hydrogen bonds: C:E.416, C:E.416, C:A.442, C:M.445, C:H.447, E:G.277, E:G.277, E:A.278, E:G.279, E:K.280, E:S.281, E:S.281, E:S.282, E:S.282, E:S.316, E:S.316, E:R.435 Salt bridges: C:K.441, C:R.443, E:K.280, E:K.280 ATP.21: 23 residues within 4Å: Chain F: V.275, A.276, G.277, A.278, G.279, K.280, S.281, S.282, S.316, L.317, R.435, M.456, S.457, D.458 Chain H: E.416, K.441, A.442, R.443, G.444, M.445, A.446, H.447 Ligands: MG.23 20 PLIP interactions: 13 interactions with chain F, 7 interactions with chain H Hydrogen bonds: F:G.277, F:G.277, F:A.278, F:G.279, F:K.280, F:S.281, F:S.282, F:S.282, F:S.316, F:S.316, F:R.435, H:E.416, H:E.416, H:A.442, H:M.445, H:H.447 Salt bridges: F:K.280, F:K.280, H:K.441, H:R.443 ATP.25: 23 residues within 4Å: Chain E: E.416, K.441, A.442, R.443, G.444, M.445, A.446, H.447 Chain G: V.275, A.276, G.277, A.278, G.279, K.280, S.281, S.282, S.316, L.317, R.435, M.456, S.457, D.458 Ligands: MG.27 21 PLIP interactions: 14 interactions with chain G, 7 interactions with chain E Hydrogen bonds: G:G.277, G:G.277, G:A.278, G:G.279, G:K.280, G:S.281, G:S.281, G:S.282, G:S.282, G:S.316, G:S.316, G:R.435, E:E.416, E:E.416, E:A.442, E:M.445, E:H.447 Salt bridges: G:K.280, G:K.280, E:K.441, E:R.443 ATP.29: 24 residues within 4Å: Chain H: V.275, A.276, G.277, A.278, G.279, K.280, S.281, S.282, S.316, L.317, L.401, R.435, M.456, S.457, D.458 Chain J: E.416, K.441, A.442, R.443, G.444, M.445, A.446, H.447 Ligands: MG.31 20 PLIP interactions: 7 interactions with chain J, 13 interactions with chain H Hydrogen bonds: J:E.416, J:E.416, J:A.442, J:M.445, J:H.447, H:G.277, H:G.277, H:A.278, H:G.279, H:K.280, H:S.281, H:S.282, H:S.282, H:S.316, H:S.316, H:R.435 Salt bridges: J:K.441, J:R.443, H:K.280, H:K.280 ATP.33: 23 residues within 4Å: Chain G: E.416, K.441, A.442, R.443, G.444, M.445, A.446, H.447 Chain I: V.275, A.276, G.277, A.278, G.279, K.280, S.281, S.282, S.316, L.317, R.435, M.456, S.457, D.458 Ligands: MG.35 21 PLIP interactions: 14 interactions with chain I, 7 interactions with chain G Hydrogen bonds: I:G.277, I:G.277, I:A.278, I:G.279, I:K.280, I:S.281, I:S.281, I:S.282, I:S.282, I:S.316, I:S.316, I:R.435, G:E.416, G:E.416, G:A.442, G:M.445, G:H.447 Salt bridges: I:K.280, I:K.280, G:K.441, G:R.443 ATP.37: 24 residues within 4Å: Chain J: V.275, A.276, G.277, A.278, G.279, K.280, S.281, S.282, S.316, L.317, L.401, R.435, M.456, S.457, D.458 Chain L: E.416, K.441, A.442, R.443, G.444, M.445, A.446, H.447 Ligands: MG.39 20 PLIP interactions: 7 interactions with chain L, 13 interactions with chain J Hydrogen bonds: L:E.416, L:E.416, L:A.442, L:M.445, L:H.447, J:G.277, J:G.277, J:A.278, J:G.279, J:K.280, J:S.281, J:S.282, J:S.282, J:S.316, J:S.316, J:R.435 Salt bridges: L:K.441, L:R.443, J:K.280, J:K.280 ATP.41: 23 residues within 4Å: Chain I: E.416, K.441, A.442, R.443, G.444, M.445, A.446, H.447 Chain K: V.275, A.276, G.277, A.278, G.279, K.280, S.281, S.282, S.316, L.317, R.435, M.456, S.457, D.458 Ligands: MG.43 21 PLIP interactions: 14 interactions with chain K, 7 interactions with chain I Hydrogen bonds: K:G.277, K:G.277, K:A.278, K:G.279, K:K.280, K:S.281, K:S.281, K:S.282, K:S.282, K:S.316, K:S.316, K:R.435, I:E.416, I:E.416, I:A.442, I:M.445, I:H.447 Salt bridges: K:K.280, K:K.280, I:K.441, I:R.443 ATP.45: 23 residues within 4Å: Chain A: E.416, K.441, A.442, R.443, G.444, M.445, A.446, H.447 Chain L: V.275, A.276, G.277, A.278, G.279, K.280, S.281, S.282, S.316, L.317, R.435, M.456, S.457, D.458 Ligands: MG.47 20 PLIP interactions: 13 interactions with chain L, 7 interactions with chain A Hydrogen bonds: L:G.277, L:G.277, L:A.278, L:G.279, L:K.280, L:S.281, L:S.282, L:S.282, L:S.316, L:S.316, L:R.435, A:E.416, A:E.416, A:A.442, A:M.445, A:H.447 Salt bridges: L:K.280, L:K.280, A:K.441, A:R.443

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

ADP.2: 21 residues within 4Å: Chain A: A.35, G.36, C.37, G.38, K.39, T.40, L.41, S.76, L.77, R.203, I.224, D.225, T.226 Chain D: K.209, Y.210, R.211, G.212, T.213, A.214, H.215 Ligands: MG.4 20 PLIP interactions: 16 interactions with chain A, 4 interactions with chain D Hydrogen bonds: A:S.34, A:G.36, A:G.36, A:C.37, A:G.38, A:K.39, A:T.40, A:T.40, A:L.41, A:S.76, A:R.203, D:Y.210, D:R.211 Water bridges: A:K.39, A:K.39, A:T.40, A:T.40, D:R.211 Salt bridges: A:K.39, D:K.209 ADP.6: 21 residues within 4Å: Chain B: A.35, G.36, C.37, G.38, K.39, T.40, L.41, S.76, L.77, R.203, I.224, D.225, T.226 Chain K: K.209, Y.210, R.211, G.212, T.213, A.214, H.215 Ligands: MG.8 20 PLIP interactions: 5 interactions with chain K, 15 interactions with chain B Hydrogen bonds: K:Y.210, K:R.211, K:T.213, B:S.34, B:G.36, B:G.36, B:C.37, B:G.38, B:K.39, B:T.40, B:T.40, B:L.41, B:S.76, B:R.203 Water bridges: K:R.211, B:K.39, B:K.39, B:T.40 Salt bridges: K:K.209, B:K.39 ADP.10: 21 residues within 4Å: Chain B: K.209, Y.210, R.211, G.212, T.213, A.214, H.215 Chain C: A.35, G.36, C.37, G.38, K.39, T.40, L.41, S.76, L.77, R.203, I.224, D.225, T.226 Ligands: MG.12 19 PLIP interactions: 4 interactions with chain B, 15 interactions with chain C Hydrogen bonds: B:Y.210, B:R.211, C:S.34, C:G.36, C:G.36, C:C.37, C:G.38, C:K.39, C:T.40, C:T.40, C:L.41, C:S.76, C:R.203 Water bridges: B:R.211, C:K.39, C:K.39, C:T.40 Salt bridges: B:K.209, C:K.39 ADP.14: 21 residues within 4Å: Chain D: A.35, G.36, C.37, G.38, K.39, T.40, L.41, S.76, L.77, R.203, I.224, D.225, T.226 Chain F: K.209, Y.210, R.211, G.212, T.213, A.214, H.215 Ligands: MG.16 21 PLIP interactions: 16 interactions with chain D, 5 interactions with chain F Hydrogen bonds: D:S.34, D:G.36, D:G.36, D:C.37, D:G.38, D:K.39, D:T.40, D:T.40, D:L.41, D:S.76, D:R.203, F:Y.210, F:R.211 Water bridges: D:K.39, D:K.39, D:T.40, D:T.40, F:R.211 Salt bridges: D:K.39, F:K.209, F:R.211 ADP.18: 21 residues within 4Å: Chain C: K.209, Y.210, R.211, G.212, T.213, A.214, H.215 Chain E: A.35, G.36, C.37, G.38, K.39, T.40, L.41, S.76, L.77, R.203, I.224, D.225, T.226 Ligands: MG.20 19 PLIP interactions: 4 interactions with chain C, 15 interactions with chain E Hydrogen bonds: C:Y.210, C:R.211, E:S.34, E:G.36, E:G.36, E:C.37, E:G.38, E:K.39, E:T.40, E:T.40, E:L.41, E:S.76, E:R.203 Water bridges: C:R.211, E:K.39, E:K.39, E:T.40 Salt bridges: C:K.209, E:K.39 ADP.22: 21 residues within 4Å: Chain F: A.35, G.36, C.37, G.38, K.39, T.40, L.41, S.76, L.77, R.203, I.224, D.225, T.226 Chain H: K.209, Y.210, R.211, G.212, T.213, A.214, H.215 Ligands: MG.24 21 PLIP interactions: 16 interactions with chain F, 5 interactions with chain H Hydrogen bonds: F:S.34, F:G.36, F:G.36, F:C.37, F:G.38, F:K.39, F:T.40, F:T.40, F:L.41, F:S.76, F:R.203, H:Y.210, H:R.211 Water bridges: F:K.39, F:K.39, F:T.40, F:T.40, H:R.211 Salt bridges: F:K.39, H:K.209, H:R.211 ADP.26: 21 residues within 4Å: Chain E: K.209, Y.210, R.211, G.212, T.213, A.214, H.215 Chain G: A.35, G.36, C.37, G.38, K.39, T.40, L.41, S.76, L.77, R.203, I.224, D.225, T.226 Ligands: MG.28 20 PLIP interactions: 15 interactions with chain G, 5 interactions with chain E Hydrogen bonds: G:S.34, G:G.36, G:G.36, G:C.37, G:G.38, G:K.39, G:T.40, G:T.40, G:L.41, G:S.76, G:R.203, E:Y.210, E:R.211 Water bridges: G:K.39, G:K.39, G:T.40, E:R.211 Salt bridges: G:K.39, E:K.209, E:R.211 ADP.30: 21 residues within 4Å: Chain H: A.35, G.36, C.37, G.38, K.39, T.40, L.41, S.76, L.77, R.203, I.224, D.225, T.226 Chain J: K.209, Y.210, R.211, G.212, T.213, A.214, H.215 Ligands: MG.32 20 PLIP interactions: 16 interactions with chain H, 4 interactions with chain J Hydrogen bonds: H:S.34, H:G.36, H:G.36, H:C.37, H:G.38, H:K.39, H:T.40, H:T.40, H:L.41, H:S.76, H:R.203, J:Y.210, J:R.211 Water bridges: H:K.39, H:K.39, H:T.40, H:T.40, J:R.211 Salt bridges: H:K.39, J:K.209 ADP.34: 21 residues within 4Å: Chain G: K.209, Y.210, R.211, G.212, T.213, A.214, H.215 Chain I: A.35, G.36, C.37, G.38, K.39, T.40, L.41, S.76, L.77, R.203, I.224, D.225, T.226 Ligands: MG.36 20 PLIP interactions: 15 interactions with chain I, 5 interactions with chain G Hydrogen bonds: I:S.34, I:G.36, I:G.36, I:C.37, I:G.38, I:K.39, I:T.40, I:T.40, I:L.41, I:S.76, I:R.203, G:Y.210, G:R.211 Water bridges: I:K.39, I:K.39, I:T.40, G:R.211 Salt bridges: I:K.39, G:K.209, G:R.211 ADP.38: 21 residues within 4Å: Chain J: A.35, G.36, C.37, G.38, K.39, T.40, L.41, S.76, L.77, R.203, I.224, D.225, T.226 Chain L: K.209, Y.210, R.211, G.212, T.213, A.214, H.215 Ligands: MG.40 20 PLIP interactions: 16 interactions with chain J, 4 interactions with chain L Hydrogen bonds: J:S.34, J:G.36, J:G.36, J:C.37, J:G.38, J:K.39, J:T.40, J:T.40, J:L.41, J:S.76, J:R.203, L:Y.210, L:R.211 Water bridges: J:K.39, J:K.39, J:T.40, J:T.40, L:R.211 Salt bridges: J:K.39, L:K.209 ADP.42: 21 residues within 4Å: Chain I: K.209, Y.210, R.211, G.212, T.213, A.214, H.215 Chain K: A.35, G.36, C.37, G.38, K.39, T.40, L.41, S.76, L.77, R.203, I.224, D.225, T.226 Ligands: MG.44 19 PLIP interactions: 15 interactions with chain K, 4 interactions with chain I Hydrogen bonds: K:S.34, K:G.36, K:G.36, K:C.37, K:G.38, K:K.39, K:T.40, K:T.40, K:L.41, K:S.76, K:R.203, I:Y.210, I:R.211 Water bridges: K:K.39, K:K.39, K:T.40, I:R.211 Salt bridges: K:K.39, I:K.209 ADP.46: 21 residues within 4Å: Chain A: K.209, Y.210, R.211, G.212, T.213, A.214, H.215 Chain L: A.35, G.36, C.37, G.38, K.39, T.40, L.41, S.76, L.77, R.203, I.224, D.225, T.226 Ligands: MG.48 21 PLIP interactions: 16 interactions with chain L, 5 interactions with chain A Hydrogen bonds: L:S.34, L:G.36, L:G.36, L:C.37, L:G.38, L:K.39, L:T.40, L:T.40, L:L.41, L:S.76, L:R.203, A:Y.210, A:R.211, A:T.213 Water bridges: L:K.39, L:K.39, L:T.40, L:T.40, A:R.211 Salt bridges: L:K.39, A:K.209

24 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 2 residues within 4Å: Chain A: S.281 Ligands: ATP.1 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:S.281, H2O.1, H2O.1 MG.4: 3 residues within 4Å: Chain A: T.40 Chain D: R.211 Ligands: ADP.2 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:T.40, H2O.1, H2O.1, H2O.1, H2O.1 MG.7: 2 residues within 4Å: Chain B: S.281 Ligands: ATP.5 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:S.281, H2O.1, H2O.1 MG.8: 4 residues within 4Å: Chain B: K.39, T.40 Chain K: R.211 Ligands: ADP.6 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:T.40, H2O.1, H2O.1, H2O.1, H2O.3 MG.11: 2 residues within 4Å: Chain C: S.281 Ligands: ATP.9 3 PLIP interactions: 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:S.281, H2O.1, H2O.1 MG.12: 4 residues within 4Å: Chain B: R.211 Chain C: K.39, T.40 Ligands: ADP.10 5 PLIP interactions: 1 interactions with chain C, 4 Ligand-Water interactions Metal complexes: C:T.40, H2O.1, H2O.1, H2O.1, H2O.1 MG.15: 2 residues within 4Å: Chain D: S.281 Ligands: ATP.13 3 PLIP interactions: 1 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:S.281, H2O.1, H2O.1 MG.16: 3 residues within 4Å: Chain D: T.40 Chain F: R.211 Ligands: ADP.14 5 PLIP interactions: 1 interactions with chain D, 4 Ligand-Water interactions Metal complexes: D:T.40, H2O.1, H2O.1, H2O.1, H2O.2 MG.19: 2 residues within 4Å: Chain E: S.281 Ligands: ATP.17 3 PLIP interactions: 1 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:S.281, H2O.1, H2O.2 MG.20: 4 residues within 4Å: Chain C: R.211 Chain E: K.39, T.40 Ligands: ADP.18 5 PLIP interactions: 1 interactions with chain E, 4 Ligand-Water interactions Metal complexes: E:T.40, H2O.1, H2O.1, H2O.1, H2O.2 MG.23: 2 residues within 4Å: Chain F: S.281 Ligands: ATP.21 3 PLIP interactions: 1 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:S.281, H2O.2, H2O.2 MG.24: 4 residues within 4Å: Chain F: K.39, T.40 Chain H: R.211 Ligands: ADP.22 5 PLIP interactions: 1 interactions with chain F, 4 Ligand-Water interactions Metal complexes: F:T.40, H2O.2, H2O.2, H2O.2, H2O.2 MG.27: 2 residues within 4Å: Chain G: S.281 Ligands: ATP.25 3 PLIP interactions: 1 interactions with chain G, 2 Ligand-Water interactions Metal complexes: G:S.281, H2O.2, H2O.2 MG.28: 4 residues within 4Å: Chain E: R.211 Chain G: K.39, T.40 Ligands: ADP.26 5 PLIP interactions: 1 interactions with chain G, 4 Ligand-Water interactions Metal complexes: G:T.40, H2O.2, H2O.2, H2O.2, H2O.2 MG.31: 2 residues within 4Å: Chain H: S.281 Ligands: ATP.29 3 PLIP interactions: 1 interactions with chain H, 2 Ligand-Water interactions Metal complexes: H:S.281, H2O.2, H2O.2 MG.32: 3 residues within 4Å: Chain H: T.40 Chain J: R.211 Ligands: ADP.30 5 PLIP interactions: 1 interactions with chain H, 4 Ligand-Water interactions Metal complexes: H:T.40, H2O.2, H2O.2, H2O.2, H2O.3 MG.35: 2 residues within 4Å: Chain I: S.281 Ligands: ATP.33 3 PLIP interactions: 1 interactions with chain I, 2 Ligand-Water interactions Metal complexes: I:S.281, H2O.2, H2O.2 MG.36: 4 residues within 4Å: Chain G: R.211 Chain I: K.39, T.40 Ligands: ADP.34 5 PLIP interactions: 1 interactions with chain I, 4 Ligand-Water interactions Metal complexes: I:T.40, H2O.2, H2O.2, H2O.2, H2O.2 MG.39: 2 residues within 4Å: Chain J: S.281 Ligands: ATP.37 3 PLIP interactions: 1 interactions with chain J, 2 Ligand-Water interactions Metal complexes: J:S.281, H2O.3, H2O.3 MG.40: 4 residues within 4Å: Chain J: K.39, T.40 Chain L: R.211 Ligands: ADP.38 5 PLIP interactions: 1 interactions with chain J, 4 Ligand-Water interactions Metal complexes: J:T.40, H2O.3, H2O.3, H2O.3, H2O.3 MG.43: 2 residues within 4Å: Chain K: S.281 Ligands: ATP.41 3 PLIP interactions: 1 interactions with chain K, 2 Ligand-Water interactions Metal complexes: K:S.281, H2O.3, H2O.3 MG.44: 4 residues within 4Å: Chain I: R.211 Chain K: K.39, T.40 Ligands: ADP.42 5 PLIP interactions: 1 interactions with chain K, 4 Ligand-Water interactions Metal complexes: K:T.40, H2O.3, H2O.3, H2O.3, H2O.3 MG.47: 2 residues within 4Å: Chain L: S.281 Ligands: ATP.45 3 PLIP interactions: 1 interactions with chain L, 2 Ligand-Water interactions Metal complexes: L:S.281, H2O.3, H2O.3 MG.48: 4 residues within 4Å: Chain A: R.211 Chain L: K.39, T.40 Ligands: ADP.46 5 PLIP interactions: 1 interactions with chain L, 4 Ligand-Water interactions Metal complexes: L:T.40, H2O.3, H2O.3, H2O.3, H2O.3

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pitsawong, W. et al., From primordial clocks to circadian oscillators. Nature (2023)

Release Date

2023-03-22

Peptides

Circadian clock protein KaiC: ABCDEFGHIJKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

J
J

K
K

L
L

Circadian clock protein KaiC

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