SMTL ID : 4dug.1

Crystal Structure of Circadian Clock Protein KaiC E318A Mutant

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.29 Å

Oligo State

homo-hexamer

Ligands

12 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: T.295, E.319 Chain B: R.459 Ligands: ATP.2 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:T.295, A:E.319, H2O.1 MG.4: 3 residues within 4Å: Chain A: T.53, D.145 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 Chain C: R.459 Ligands: ATP.6 No protein-ligand interaction detected (PLIP) MG.8: 4 residues within 4Å: Chain B: K.52, T.53, D.145 Ligands: ATP.7 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:T.53, H2O.1 MG.9: 2 residues within 4Å: Chain C: T.295 Ligands: ATP.10 2 PLIP interactions: 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:T.295, H2O.2 MG.12: 5 residues within 4Å: Chain C: T.53, E.78, D.145 Chain D: R.226 Ligands: ATP.11 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:T.53, C:E.78 MG.14: 4 residues within 4Å: Chain D: T.295, E.319, D.378 Ligands: ATP.15 2 PLIP interactions: 1 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:T.295, H2O.2 MG.17: 5 residues within 4Å: Chain D: K.52, T.53, D.145, T.181 Ligands: ATP.16 3 PLIP interactions: 1 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:T.53, H2O.2, H2O.2 MG.18: 3 residues within 4Å: Chain E: T.295, D.378 Ligands: ATP.19 2 PLIP interactions: 1 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:T.295, H2O.3 MG.21: 4 residues within 4Å: Chain E: T.53, E.78, D.145 Ligands: ATP.20 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:T.53, E:D.145 MG.22: 5 residues within 4Å: Chain A: R.459 Chain F: T.295, E.319, D.378 Ligands: ATP.23 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:T.295 MG.25: 3 residues within 4Å: Chain F: T.53, D.145 Ligands: ATP.24 2 PLIP interactions: 1 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:T.53, H2O.3

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

ATP.2: 23 residues within 4Å: Chain A: T.290, G.291, T.292, G.293, K.294, T.295, L.296, W.331, T.415, Y.442, R.451, I.472, S.473, D.474 Chain B: T.432, K.457, M.458, R.459, G.460, S.461, W.462, H.463 Ligands: MG.1 17 PLIP interactions: 12 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:G.291, A:G.293, A:K.294, A:T.295, A:L.296, A:T.415, A:Y.442, A:R.451, A:R.451, A:D.474, B:M.458, B:H.463 Salt bridges: A:K.294, A:K.294, B:K.457, B:K.457, B:R.459 ATP.3: 22 residues within 4Å: Chain A: G.49, T.50, G.51, K.52, T.53, L.54, S.89, F.90, R.218, I.239, T.240, D.241 Chain B: L.223, K.224, L.225, R.226, G.227, T.228, S.229, H.230, K.232 Ligands: MG.4 18 PLIP interactions: 12 interactions with chain A, 6 interactions with chain B Hydrogen bonds: A:G.49, A:T.50, A:G.51, A:K.52, A:T.53, A:L.54, A:R.218, A:R.218, A:D.241, A:D.241, B:L.223, B:L.225, B:H.230 Salt bridges: A:K.52, A:K.52, B:K.224, B:K.224, B:R.226 ATP.6: 20 residues within 4Å: Chain B: T.290, G.291, T.292, G.293, K.294, T.295, L.296, S.330, W.331, T.415, R.451, I.472 Chain C: T.432, K.457, M.458, R.459, S.461, W.462, H.463 Ligands: MG.5 21 PLIP interactions: 6 interactions with chain C, 15 interactions with chain B Hydrogen bonds: C:M.458, C:G.460, C:H.463, B:G.291, B:G.291, B:T.292, B:G.293, B:K.294, B:T.295, B:T.295, B:L.296, B:T.415, B:T.415, B:R.451, B:R.451 Salt bridges: C:K.457, C:K.457, C:R.459, B:K.294, B:K.294 Water bridges: B:E.319 ATP.7: 22 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, T.240, D.241 Chain C: L.223, K.224, L.225, R.226, G.227, T.228, S.229, H.230 Ligands: MG.8 22 PLIP interactions: 16 interactions with chain B, 6 interactions with chain C Hydrogen bonds: B:T.47, B:G.49, 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:R.218, B:D.241, B:D.241, C:L.225, C:H.230, C:K.232 Salt bridges: B:K.52, B:K.52, C:K.224, C:K.224, C:R.226 ATP.10: 23 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, D.474 Chain D: K.457, M.458, R.459, G.460, S.461, W.462, H.463, K.465 Ligands: MG.9 22 PLIP interactions: 6 interactions with chain D, 16 interactions with chain C Hydrogen bonds: D:M.458, D:H.463, C:T.290, C:G.291, C:G.291, C:T.292, C:G.293, C:K.294, C:T.295, C:T.295, C:T.295, C:L.296, C:R.451, C:R.451, C:D.474, C:D.474 Water bridges: D:R.459, D:R.459 Salt bridges: D:K.457, D:R.459, C:K.294, C:K.294 ATP.11: 24 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, T.240, D.241 Chain D: F.199, L.223, K.224, L.225, R.226, G.227, T.228, S.229, H.230, K.232 Ligands: MG.12 20 PLIP interactions: 6 interactions with chain D, 14 interactions with chain C Hydrogen bonds: D:L.225, D:H.230, D:K.232, C:G.49, C:G.49, C:T.50, C:T.50, C:G.51, C:K.52, C:T.53, C:T.53, C:L.54, C:R.218, C:D.241, C:D.241 Salt bridges: D:K.224, D:K.224, D:R.226, C:K.52, C:K.52 ATP.15: 21 residues within 4Å: Chain D: T.290, G.291, T.292, G.293, K.294, T.295, L.296, S.330, W.331, R.451, I.472, D.474 Chain E: T.432, K.457, M.458, R.459, G.460, S.461, W.462, H.463 Ligands: MG.14 17 PLIP interactions: 13 interactions with chain D, 4 interactions with chain E Hydrogen bonds: D:T.290, D:T.290, D:G.291, D:G.291, D:T.292, D:T.295, D:L.296, D:R.451, D:R.451, D:D.474, D:D.474, E:M.458, E:H.463 Salt bridges: D:K.294, D:K.294, E:K.457, E:R.459 ATP.16: 23 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: F.199, L.223, K.224, L.225, R.226, G.227, T.228, S.229, H.230, K.232 Ligands: MG.17 21 PLIP interactions: 7 interactions with chain E, 14 interactions with chain D Hydrogen bonds: E:L.225, E:H.230, E:K.232, D:G.49, D:G.49, D:T.50, D:G.51, D:K.52, D:T.53, D:L.54, D:S.89, D:S.89, D:R.218, D:R.218, D:D.241 Water bridges: E:R.226 Salt bridges: E:K.224, E:K.224, E:R.226, D:K.52, D:K.52 ATP.19: 21 residues within 4Å: Chain E: 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: F.456, K.457, M.458, R.459, S.461, W.462, H.463, K.465 Ligands: MG.18 19 PLIP interactions: 14 interactions with chain E, 5 interactions with chain F Hydrogen bonds: E:T.290, E:T.290, E:G.291, E:G.291, E:G.293, E:K.294, E:T.295, E:L.296, E:S.330, E:T.415, E:R.451, E:R.451, F:M.458, F:H.463, F:K.465 Salt bridges: E:K.294, E:K.294, F:K.457, F:R.459 ATP.20: 21 residues within 4Å: Chain E: G.49, T.50, G.51, K.52, T.53, L.54, E.78, S.89, F.90, R.218, I.239, D.241 Chain F: L.223, K.224, L.225, R.226, T.228, S.229, H.230, K.232 Ligands: MG.21 22 PLIP interactions: 7 interactions with chain F, 15 interactions with chain E Hydrogen bonds: F:L.225, F:H.230, F:K.232, E:G.49, E:G.49, E:T.50, E:G.51, E:K.52, E:T.53, E:L.54, E:E.78, E:S.89, E:S.89, E:R.218, E:D.241 Water bridges: F:R.226, E:E.183 Salt bridges: F:K.224, F:K.224, F:R.226, E:K.52, E:K.52 ATP.23: 22 residues within 4Å: Chain A: K.457, M.458, R.459, G.460, S.461, W.462, H.463, K.465 Chain F: T.290, G.291, T.292, G.293, K.294, T.295, L.296, S.330, W.331, R.451, I.472, S.473, D.474 Ligands: MG.22 16 PLIP interactions: 11 interactions with chain F, 5 interactions with chain A Hydrogen bonds: F:G.291, F:G.291, F:G.293, F:K.294, F:T.295, F:L.296, F:R.451, F:R.451, F:D.474, A:M.458, A:H.463, A:K.465 Salt bridges: F:K.294, F:K.294, A:K.457, A:R.459 ATP.24: 21 residues within 4Å: Chain A: L.223, K.224, L.225, R.226, T.228, S.229, H.230, K.232 Chain F: G.49, T.50, G.51, K.52, T.53, L.54, E.78, S.89, F.90, I.239, T.240, D.241 Ligands: MG.25 20 PLIP interactions: 13 interactions with chain F, 7 interactions with chain A Hydrogen bonds: F:G.49, F:G.49, F:T.50, F:G.51, F:K.52, F:T.53, F:L.54, F:E.78, F:S.89, F:D.241, A:L.225, A:H.230, A:K.232 Water bridges: F:K.52, A:K.224 Salt bridges: F:K.52, F:K.52, A:K.224, A:K.224, A:R.226

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.13: 7 residues within 4Å: Chain C: T.47, I.185, E.187, R.216 Chain D: G.189, I.191, L.223 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:T.47, D:G.189 Water bridges: C:E.187, C:E.187 Salt bridges: C:R.216

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Egli, M. et al., Dephosphorylation of the Core Clock Protein KaiC in the Cyanobacterial KaiABC Circadian Oscillator Proceeds via an ATP Synthase Mechanism. Biochemistry (2012)

Release Date

2012-03-14

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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