SMTL ID : 8db3.1

Crystal structure of KaiC with truncated C-terminal coiled-coil domain

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

homo-hexamer

Ligands

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

ADP.1: 22 residues within 4Å: Chain A: V.273, A.274, G.275, A.276, G.277, K.278, S.279, S.280, M.312, S.314, L.315, R.433, M.454, S.455, D.456 Chain B: K.439, A.440, R.441, G.442, M.443, A.444, H.445 14 PLIP interactions: 12 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:V.273, A:G.275, A:G.275, A:A.276, A:G.277, A:K.278, A:S.279, A:S.280, A:R.433, A:R.433, A:D.456, B:A.440, B:M.443 Salt bridges: A:K.278 ADP.2: 24 residues within 4Å: Chain A: S.32, A.33, G.34, C.35, G.36, K.37, T.38, L.39, N.71, V.72, S.74, L.75, R.201, I.222, D.223, T.224 Chain B: V.206, K.207, Y.208, R.209, G.210, T.211, A.212, H.213 23 PLIP interactions: 8 interactions with chain B, 15 interactions with chain A Hydrogen bonds: B:Y.208, B:G.210, B:T.211, B:H.213, B:H.213, A:S.32, A:G.34, A:C.35, A:G.36, A:K.37, A:T.38, A:T.38, A:T.38, A:L.39, A:N.71, A:S.74, A:L.75, A:R.201, A:R.201 Salt bridges: B:K.207, B:R.209, B:R.209, A:K.37 ADP.3: 24 residues within 4Å: Chain B: S.32, A.33, G.34, C.35, G.36, K.37, T.38, L.39, N.71, V.72, S.74, L.75, R.201, I.222, D.223 Chain C: V.206, K.207, Y.208, R.209, G.210, T.211, A.212, H.213, T.215 21 PLIP interactions: 14 interactions with chain B, 7 interactions with chain C Hydrogen bonds: B:S.32, B:S.32, B:G.34, B:G.34, B:C.35, B:G.36, B:K.37, B:T.38, B:T.38, B:L.39, B:N.71, B:R.201, B:R.201, C:Y.208, C:G.210, C:T.211, C:H.213 Salt bridges: B:K.37, C:K.207, C:R.209, C:R.209 ADP.4: 22 residues within 4Å: Chain B: V.273, A.274, G.275, A.276, G.277, K.278, S.279, S.280, M.312, S.314, L.315, R.433, M.454, S.455, D.456 Chain C: K.439, A.440, R.441, G.442, M.443, A.444, H.445 16 PLIP interactions: 2 interactions with chain C, 14 interactions with chain B Hydrogen bonds: C:A.440, C:H.445, B:V.273, B:G.275, B:A.276, B:G.277, B:K.278, B:S.279, B:S.279, B:S.279, B:S.280, B:S.280, B:S.314, B:S.314, B:R.433 Salt bridges: B:K.278 ADP.5: 22 residues within 4Å: Chain C: V.273, A.274, G.275, A.276, G.277, K.278, S.279, S.280, M.312, S.314, L.315, R.433, M.454, S.455, D.456 Chain D: K.439, A.440, R.441, G.442, M.443, A.444, H.445 17 PLIP interactions: 14 interactions with chain C, 3 interactions with chain D Hydrogen bonds: C:V.273, C:G.275, C:G.275, C:A.276, C:G.277, C:K.278, C:S.279, C:S.279, C:S.279, C:S.280, C:S.280, C:S.314, C:R.433, D:K.439, D:A.440, D:H.445 Salt bridges: C:K.278 ADP.6: 25 residues within 4Å: Chain C: S.32, A.33, G.34, C.35, G.36, K.37, T.38, L.39, N.71, V.72, S.74, L.75, R.201, I.222, D.223, T.224 Chain D: V.206, K.207, Y.208, R.209, G.210, T.211, A.212, H.213, T.215 20 PLIP interactions: 13 interactions with chain C, 7 interactions with chain D Hydrogen bonds: C:S.32, C:G.34, C:C.35, C:G.36, C:K.37, C:T.38, C:T.38, C:T.38, C:L.39, C:N.71, C:S.74, C:R.201, D:Y.208, D:G.210, D:T.211, D:H.213 Salt bridges: C:K.37, D:K.207, D:R.209, D:R.209 ADP.7: 22 residues within 4Å: Chain D: V.273, A.274, G.275, A.276, G.277, K.278, S.279, S.280, M.312, S.314, L.315, R.433, M.454, S.455, D.456 Chain E: K.439, A.440, R.441, G.442, M.443, A.444, H.445 14 PLIP interactions: 12 interactions with chain D, 2 interactions with chain E Hydrogen bonds: D:V.273, D:G.275, D:G.275, D:A.276, D:G.277, D:K.278, D:S.279, D:S.280, D:R.433, D:R.433, D:D.456, E:A.440, E:M.443 Salt bridges: D:K.278 ADP.8: 24 residues within 4Å: Chain D: S.32, A.33, G.34, C.35, G.36, K.37, T.38, L.39, N.71, V.72, S.74, L.75, R.201, I.222, D.223, T.224 Chain E: V.206, K.207, Y.208, R.209, G.210, T.211, A.212, H.213 23 PLIP interactions: 8 interactions with chain E, 15 interactions with chain D Hydrogen bonds: E:Y.208, E:G.210, E:T.211, E:H.213, E:H.213, D:S.32, D:G.34, D:C.35, D:G.36, D:K.37, D:T.38, D:T.38, D:T.38, D:L.39, D:N.71, D:S.74, D:L.75, D:R.201, D:R.201 Salt bridges: E:K.207, E:R.209, E:R.209, D:K.37 ADP.9: 24 residues within 4Å: Chain E: S.32, A.33, G.34, C.35, G.36, K.37, T.38, L.39, N.71, V.72, S.74, L.75, R.201, I.222, D.223 Chain F: V.206, K.207, Y.208, R.209, G.210, T.211, A.212, H.213, T.215 21 PLIP interactions: 7 interactions with chain F, 14 interactions with chain E Hydrogen bonds: F:Y.208, F:G.210, F:T.211, F:H.213, E:S.32, E:S.32, E:G.34, E:G.34, E:C.35, E:G.36, E:K.37, E:T.38, E:T.38, E:L.39, E:N.71, E:R.201, E:R.201 Salt bridges: F:K.207, F:R.209, F:R.209, E:K.37 ADP.10: 22 residues within 4Å: Chain E: V.273, A.274, G.275, A.276, G.277, K.278, S.279, S.280, M.312, S.314, L.315, R.433, M.454, S.455, D.456 Chain F: K.439, A.440, R.441, G.442, M.443, A.444, H.445 16 PLIP interactions: 14 interactions with chain E, 2 interactions with chain F Hydrogen bonds: E:V.273, E:G.275, E:A.276, E:G.277, E:K.278, E:S.279, E:S.279, E:S.279, E:S.280, E:S.280, E:S.314, E:S.314, E:R.433, F:A.440, F:H.445 Salt bridges: E:K.278 ADP.11: 22 residues within 4Å: Chain A: K.439, A.440, R.441, G.442, M.443, A.444, H.445 Chain F: V.273, A.274, G.275, A.276, G.277, K.278, S.279, S.280, M.312, S.314, L.315, R.433, M.454, S.455, D.456 17 PLIP interactions: 14 interactions with chain F, 3 interactions with chain A Hydrogen bonds: F:V.273, F:G.275, F:G.275, F:A.276, F:G.277, F:K.278, F:S.279, F:S.279, F:S.279, F:S.280, F:S.280, F:S.314, F:R.433, A:K.439, A:A.440, A:H.445 Salt bridges: F:K.278 ADP.12: 25 residues within 4Å: Chain A: V.206, K.207, Y.208, R.209, G.210, T.211, A.212, H.213, T.215 Chain F: S.32, A.33, G.34, C.35, G.36, K.37, T.38, L.39, N.71, V.72, S.74, L.75, R.201, I.222, D.223, T.224 20 PLIP interactions: 13 interactions with chain F, 7 interactions with chain A Hydrogen bonds: F:S.32, F:G.34, F:C.35, F:G.36, F:K.37, F:T.38, F:T.38, F:T.38, F:L.39, F:N.71, F:S.74, F:R.201, A:Y.208, A:G.210, A:T.211, A:H.213 Salt bridges: F:K.37, A:K.207, A:R.209, A:R.209

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: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
A

E
B

F
C

Circadian clock protein KaiC