SMTL ID : 8dba.1

Crystal structure of dodecameric KaiC

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.50 Å

Oligo State

homo-12-mer

Ligands

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

ADP.1: 22 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 C: V.208, K.209, Y.210, R.211, G.212, T.213, A.214, H.215 Ligands: MG.3 12 PLIP interactions: 9 interactions with chain A, 3 interactions with chain C Hydrogen bonds: A:G.36, A:G.38, A:K.39, A:T.40, A:T.40, A:L.41, A:R.203, A:R.203, C:G.212, C:T.213, C:H.215 Salt bridges: A:K.39 ADP.4: 22 residues within 4Å: Chain A: A.276, G.277, A.278, G.279, K.280, S.281, S.282, M.314, S.316, L.317, R.435, M.456, D.458 Chain C: L.440, K.441, A.442, R.443, G.444, M.445, A.446, H.447 Ligands: MG.2 17 PLIP interactions: 12 interactions with chain A, 5 interactions with chain C Hydrogen bonds: A:G.277, A:G.279, A:K.280, A:S.281, A:S.282, A:S.316, A:S.316, A:R.435, C:L.440, C:H.447 Water bridges: A:E.304, A:E.304, A:D.364, C:R.443 Salt bridges: A:K.280, C:R.443, C:R.443 ADP.5: 23 residues within 4Å: Chain A: V.208, K.209, Y.210, R.211, G.212, T.213, A.214, H.215, T.217 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 Ligands: MG.7 18 PLIP interactions: 5 interactions with chain A, 13 interactions with chain B Hydrogen bonds: A:G.212, A:H.215, A:H.215, 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:S.76, B:R.203, B:R.203 Water bridges: A:R.211, B:T.40 Salt bridges: A:K.209, B:K.39 ADP.8: 22 residues within 4Å: Chain A: L.440, K.441, A.442, R.443, M.445, A.446, H.447 Chain B: A.276, G.277, A.278, G.279, K.280, S.281, S.282, M.314, S.316, L.317, R.435, M.456, S.457, D.458 Ligands: MG.6 17 PLIP interactions: 13 interactions with chain B, 4 interactions with chain A Hydrogen bonds: 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, B:R.435, A:A.442, A:A.442, A:H.447, A:H.447 Salt bridges: B:K.280 ADP.10: 24 residues within 4Å: Chain C: S.34, A.35, G.36, C.37, G.38, K.39, T.40, L.41, N.73, S.76, L.77, E.170, R.203, I.224, D.225, T.226 Chain E: K.209, Y.210, R.211, G.212, T.213, A.214, H.215 Ligands: MG.12 17 PLIP interactions: 14 interactions with chain C, 3 interactions with chain E Hydrogen bonds: C:G.36, C:G.36, C:G.38, C:K.39, C:T.40, C:T.40, C:L.41, C:S.76, C:R.203, E:G.212, E:H.215 Water bridges: C:K.39, C:T.40, C:E.170, C:E.170 Salt bridges: C:K.39, E:K.209 ADP.13: 21 residues within 4Å: Chain C: A.276, G.277, G.279, K.280, S.281, S.282, S.316, L.317, R.435, M.456, S.457, D.458 Chain E: L.440, K.441, A.442, R.443, G.444, M.445, A.446, H.447 Ligands: MG.11 11 PLIP interactions: 8 interactions with chain C, 3 interactions with chain E Hydrogen bonds: C:G.277, C:G.279, C:K.280, C:S.281, C:S.282, C:S.316, C:R.435, E:R.443, E:H.447 Salt bridges: C:K.280, E:K.441 ADP.14: 24 residues within 4Å: Chain D: A.35, G.36, C.37, G.38, K.39, T.40, L.41, N.73, S.76, L.77, R.203, I.224, D.225, T.226 Chain F: V.208, K.209, Y.210, R.211, G.212, T.213, A.214, H.215, T.217 Ligands: MG.16 21 PLIP interactions: 8 interactions with chain F, 13 interactions with chain D Hydrogen bonds: F:Y.210, F:H.215, 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:N.73, D:S.76, D:R.203 Water bridges: F:K.209, F:R.211, F:R.211, D:E.170 Salt bridges: F:K.209, F:R.211, F:R.211, D:K.39 ADP.17: 24 residues within 4Å: Chain D: A.276, G.277, A.278, G.279, K.280, S.281, S.282, E.304, M.314, S.316, L.317, R.435, M.456, S.457, D.458 Chain F: L.440, K.441, A.442, R.443, G.444, M.445, A.446, H.447 Ligands: MG.15 19 PLIP interactions: 10 interactions with chain F, 9 interactions with chain D Hydrogen bonds: F:L.440, F:A.442, F:R.443, F:M.445, F:H.447, D:G.279, D:K.280, D:S.281, D:S.282, D:E.304, D:S.316, D:R.435 Water bridges: F:S.416, F:R.443, D:S.281 Salt bridges: F:K.441, F:K.441, F:R.443, D:K.280 ADP.18: 22 residues within 4Å: Chain D: 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, N.73, S.76, L.77, R.203, I.224, D.225, T.226 Ligands: MG.20 16 PLIP interactions: 11 interactions with chain E, 5 interactions with chain D Hydrogen bonds: 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, D:G.212, D:H.215 Water bridges: E:N.73, D:K.209, D:R.211 Salt bridges: E:K.39, D:K.209 ADP.21: 23 residues within 4Å: Chain D: L.440, 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, R.435, M.456, S.457, D.458 Ligands: MG.19 18 PLIP interactions: 14 interactions with chain E, 4 interactions with chain D Hydrogen bonds: 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:R.435, E:R.435, E:D.458, D:A.442, D:R.443, D:H.447 Water bridges: E:S.281, E:E.304 Salt bridges: E:K.280, D:K.441 ADP.22: 22 residues within 4Å: Chain B: K.209, Y.210, R.211, G.212, T.213, A.214, H.215 Chain F: A.35, G.36, C.37, G.38, K.39, T.40, L.41, N.73, S.76, L.77, R.203, I.224, D.225, T.226 Ligands: MG.9 16 PLIP interactions: 11 interactions with chain F, 5 interactions with chain B Hydrogen bonds: F:G.36, F:C.37, F:G.38, F:K.39, F:T.40, F:L.41, F:S.76, F:R.203, B:G.212, B:A.214, B:H.215 Water bridges: F:T.40, F:E.170, B:K.209 Salt bridges: F:K.39, B:K.209 ADP.24: 24 residues within 4Å: Chain B: L.440, K.441, A.442, R.443, G.444, M.445, A.446, H.447 Chain F: V.275, A.276, G.277, A.278, G.279, K.280, S.281, S.282, M.314, S.316, L.317, R.435, M.456, S.457, D.458 Ligands: MG.23 15 PLIP interactions: 12 interactions with chain F, 3 interactions with chain B Hydrogen bonds: F:G.277, F:A.278, F:G.279, F:K.280, F:S.281, F:S.282, F:R.435, F:D.458, B:A.442, B:R.443, B:H.447 Water bridges: F:S.281, F:E.304, F:E.305 Salt bridges: F:K.280 ADP.25: 22 residues within 4Å: Chain G: A.35, G.36, C.37, G.38, K.39, T.40, L.41, N.73, S.76, L.77, R.203, I.224, D.225 Chain I: K.209, Y.210, R.211, G.212, T.213, A.214, H.215, T.217 Ligands: MG.27 19 PLIP interactions: 11 interactions with chain G, 8 interactions with chain I Hydrogen bonds: G:S.34, G:G.36, G:G.36, G:G.38, G:K.39, G:T.40, G:T.40, G:L.41, G:S.76, G:R.203, I:Y.210, I:G.212, I:T.213 Salt bridges: G:K.39, I:K.209, I:R.211 Water bridges: I:K.209, I:R.211, I:R.211 ADP.28: 22 residues within 4Å: 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 Chain I: K.441, A.442, R.443, G.444, M.445, A.446, H.447 Ligands: MG.26 21 PLIP interactions: 15 interactions with chain G, 6 interactions with chain I Hydrogen bonds: G:G.277, G:A.278, G:G.279, G:K.280, G:S.281, G:S.281, G:S.281, G:S.282, G:S.282, G:R.435, G:D.458, I:A.442, I:R.443, I:R.443, I:H.447 Water bridges: G:K.280, G:K.280, G:N.313 Salt bridges: G:K.280, I:K.441, I:K.441 ADP.30: 23 residues within 4Å: Chain G: V.208, K.209, Y.210, R.211, G.212, T.213, A.214, H.215, T.217 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 Ligands: MG.31 12 PLIP interactions: 2 interactions with chain G, 10 interactions with chain H Hydrogen bonds: G:G.212, G:T.213, 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:R.203 Salt bridges: H:K.39 ADP.32: 23 residues within 4Å: Chain G: K.441, A.442, R.443, G.444, M.445, A.446, H.447 Chain H: V.275, A.276, G.277, A.278, G.279, K.280, S.281, S.282, M.314, S.316, L.317, R.435, M.456, S.457, D.458 Ligands: MG.29 18 PLIP interactions: 4 interactions with chain G, 14 interactions with chain H Hydrogen bonds: G:A.442, G:M.445, G:H.447, H:G.277, H:A.278, H:G.279, H:K.280, H:S.281, H:S.281, H:S.282, H:S.282, H:R.435, H:R.435, H:D.458 Salt bridges: G:K.441, H:K.280 Water bridges: H:K.280, H:E.304 ADP.34: 23 residues within 4Å: Chain I: S.34, A.35, G.36, C.37, G.38, K.39, T.40, L.41, N.73, 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.36 20 PLIP interactions: 8 interactions with chain K, 12 interactions with chain I Hydrogen bonds: K:Y.210, K:G.212, K:G.212, K:A.214, K:H.215, I:S.34, I:S.34, I:G.36, I:C.37, I:G.38, I:K.39, I:T.40, I:T.40, I:L.41, I:R.203 Water bridges: K:K.209, I:K.39 Salt bridges: K:K.209, K:K.209, I:K.39 ADP.37: 23 residues within 4Å: Chain I: V.275, A.276, G.277, A.278, G.279, K.280, S.281, S.282, M.314, S.316, L.317, R.435, M.456, S.457, D.458 Chain K: K.441, A.442, R.443, G.444, M.445, A.446, H.447 Ligands: MG.35 20 PLIP interactions: 15 interactions with chain I, 5 interactions with chain K Hydrogen bonds: I:G.277, I:A.278, I:G.279, I:K.280, I:S.281, I:S.282, I:S.316, I:S.316, I:R.435, K:A.442, K:R.443, K:A.446, K:H.447 Water bridges: I:K.280, I:S.281, I:E.304, I:E.305 Salt bridges: I:K.280, I:K.280, K:K.441 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 Chain L: V.208, K.209, Y.210, R.211, G.212, T.213, A.214, H.215 Ligands: MG.40 18 PLIP interactions: 7 interactions with chain L, 11 interactions with chain J Hydrogen bonds: L:G.212, L:T.213, L:H.215, 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 Water bridges: L:R.211, J:K.39 Salt bridges: L:K.209, L:R.211, L:R.211, J:K.39 ADP.41: 22 residues within 4Å: Chain J: V.275, A.276, G.277, A.278, G.279, K.280, S.281, S.282, M.314, S.316, L.317, R.435, M.456, S.457, D.458 Chain L: K.441, A.442, R.443, M.445, A.446, H.447 Ligands: MG.39 19 PLIP interactions: 11 interactions with chain J, 8 interactions with chain L Hydrogen bonds: J:G.277, J:A.278, J:G.279, J:K.280, J:S.281, J:S.282, J:S.282, J:R.435, J:D.458, L:A.442, L:A.442, L:R.443, L:H.447, L:H.447 Water bridges: J:E.304, L:R.443 Salt bridges: J:K.280, L:K.441, L:R.443 ADP.42: 22 residues within 4Å: Chain J: 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, N.73, S.76, L.77, R.203, I.224, D.225, T.226 Ligands: MG.44 15 PLIP interactions: 11 interactions with chain K, 4 interactions with chain J Hydrogen bonds: K:G.36, K:C.37, K:G.38, K:K.39, K:T.40, K:T.40, K:L.41, K:N.73, K:S.76, K:R.203, J:G.212, J:T.213, J:H.215 Salt bridges: K:K.39 Water bridges: J:K.209 ADP.45: 21 residues within 4Å: Chain J: L.440, K.441, A.442, R.443, G.444, M.445, A.446, H.447 Chain K: A.276, G.277, A.278, G.279, K.280, S.281, S.282, S.316, L.317, R.435, M.456, D.458 Ligands: MG.43 19 PLIP interactions: 4 interactions with chain J, 15 interactions with chain K Hydrogen bonds: J:R.443, J:H.447, J:H.447, K:G.277, K:A.278, K:G.279, K:K.280, K:S.281, K:S.281, K:S.281, K:S.282, K:E.304, K:S.316, K:R.435, K:R.435 Salt bridges: J:K.441, K:K.280 Water bridges: K:E.304, K:E.304 ADP.46: 22 residues within 4Å: Chain H: V.208, 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, N.73, S.76, L.77, R.203, I.224, D.225, T.226 18 PLIP interactions: 12 interactions with chain L, 6 interactions with chain H Hydrogen bonds: L:G.36, L:G.38, L:K.39, L:T.40, L:T.40, L:L.41, L:R.203, H:Y.210, H:G.212, H:T.213 Water bridges: L:E.65, L:E.65, L:D.132, L:D.132, H:K.209, H:K.209 Salt bridges: L:K.39, H:K.209 ADP.47: 23 residues within 4Å: Chain H: L.440, 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.33 22 PLIP interactions: 7 interactions with chain H, 15 interactions with chain L Hydrogen bonds: H:A.442, H:A.442, H:M.445, H:H.447, L:G.277, L:A.278, L:G.279, L:K.280, L:S.281, L:S.281, L:S.282, L:S.282, L:S.316, L:R.435, L:R.435, L:D.458 Water bridges: H:R.443, H:R.443, L:E.304, L:E.304 Salt bridges: H:K.441, L:K.280

23 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 6 residues within 4Å: Chain A: K.280, E.304, L.401 Chain C: S.416, R.443 Ligands: ADP.4 3 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: A:E.304, C:S.416, H2O.1 MG.3: 4 residues within 4Å: Chain A: T.40, E.65 Chain C: R.211 Ligands: ADP.1 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:T.40, H2O.1, H2O.1 MG.6: 5 residues within 4Å: Chain B: K.280, S.281, E.304, D.364 Ligands: ADP.8 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:S.281, H2O.1, H2O.1 MG.7: 3 residues within 4Å: Chain B: T.40, E.65 Ligands: ADP.5 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:T.40, H2O.1 MG.9: 4 residues within 4Å: Chain B: R.211 Chain F: T.40, E.65 Ligands: ADP.22 2 PLIP interactions: 1 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:T.40, H2O.2 MG.11: 5 residues within 4Å: Chain C: S.281, D.364 Chain E: S.416, R.443 Ligands: ADP.13 No protein-ligand interaction detected (PLIP) MG.12: 3 residues within 4Å: Chain C: T.40, E.65 Ligands: ADP.10 No protein-ligand interaction detected (PLIP) MG.15: 7 residues within 4Å: Chain D: A.276, G.277, K.280 Chain F: S.416, K.441, R.443 Ligands: ADP.17 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:A.276 MG.16: 4 residues within 4Å: Chain D: T.40, D.132 Chain F: R.211 Ligands: ADP.14 2 PLIP interactions: 1 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:T.40, H2O.1 MG.19: 5 residues within 4Å: Chain D: R.443 Chain E: S.281, E.304, D.364 Ligands: ADP.21 2 PLIP interactions: 1 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:S.281, H2O.2 MG.20: 4 residues within 4Å: Chain D: R.211 Chain E: T.40, E.65 Ligands: ADP.18 3 PLIP interactions: 1 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:T.40, H2O.1, H2O.1 MG.23: 6 residues within 4Å: Chain B: S.416, K.441, R.443 Chain F: K.280, E.304 Ligands: ADP.24 No protein-ligand interaction detected (PLIP) MG.26: 6 residues within 4Å: Chain G: S.281, E.304, E.305, D.364 Chain I: R.443 Ligands: ADP.28 2 PLIP interactions: 1 interactions with chain G, 1 Ligand-Water interactions Metal complexes: G:S.281, H2O.2 MG.27: 3 residues within 4Å: Chain G: T.40 Chain I: R.211 Ligands: ADP.25 3 PLIP interactions: 1 interactions with chain G, 2 Ligand-Water interactions Metal complexes: G:T.40, H2O.2, H2O.2 MG.29: 5 residues within 4Å: Chain G: R.443 Chain H: S.281, E.304, E.305 Ligands: ADP.32 2 PLIP interactions: 1 interactions with chain H, 1 Ligand-Water interactions Metal complexes: H:S.281, H2O.2 MG.31: 3 residues within 4Å: Chain H: T.40, E.65 Ligands: ADP.30 4 PLIP interactions: 2 interactions with chain H, 2 Ligand-Water interactions Metal complexes: H:T.40, H:E.65, H2O.2, H2O.2 MG.33: 5 residues within 4Å: Chain H: K.441, R.443 Chain L: S.281, E.304 Ligands: ADP.47 No protein-ligand interaction detected (PLIP) MG.35: 5 residues within 4Å: Chain I: S.281, E.304, D.364 Chain K: R.443 Ligands: ADP.37 3 PLIP interactions: 2 interactions with chain I, 1 Ligand-Water interactions Metal complexes: I:S.281, I:E.304, H2O.2 MG.36: 4 residues within 4Å: Chain I: T.40 Chain K: K.209, R.211 Ligands: ADP.34 No protein-ligand interaction detected (PLIP) MG.39: 6 residues within 4Å: Chain J: K.280, S.281, E.304, P.365 Chain L: R.443 Ligands: ADP.41 4 PLIP interactions: 2 interactions with chain J, 2 Ligand-Water interactions Metal complexes: J:S.281, J:E.304, H2O.3, H2O.3 MG.40: 5 residues within 4Å: Chain J: K.39, E.170 Chain L: K.209, R.211 Ligands: ADP.38 No protein-ligand interaction detected (PLIP) MG.43: 6 residues within 4Å: Chain J: R.443 Chain K: K.280, S.281, E.304, D.364 Ligands: ADP.45 3 PLIP interactions: 1 interactions with chain K, 2 Ligand-Water interactions Metal complexes: K:S.281, H2O.3, H2O.3 MG.44: 3 residues within 4Å: Chain K: T.40, E.65 Ligands: ADP.42 2 PLIP interactions: 1 interactions with chain K, 1 Ligand-Water interactions Metal complexes: K:T.40, 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