SMTL ID : 3k0c.1

Crystal structure of the phosphorylation-site double mutant S431A/T432E of the KaiC circadian clock protein

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.30 Å

Oligo State

homo-hexamer

Ligands

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

ATP.1: 22 residues within 4Å: Chain A: 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 B: K.457, M.458, R.459, G.460, S.461, W.462, H.463, K.465 Ligands: MG.3, MG.5 21 PLIP interactions: 7 interactions with chain B, 14 interactions with chain A Hydrogen bonds: B:M.458, B:H.463, B:K.465, A:G.291, A:G.293, A:K.294, A:T.295, A:T.295, A:T.295, A:L.296, A:Y.442, A:R.451, A:R.451, A:D.474, A:D.474 Water bridges: B:R.459, B:R.459 Salt bridges: B:K.457, B:R.459, A:K.294, A:K.294 ATP.2: 25 residues within 4Å: Chain A: S.48, G.49, T.50, G.51, K.52, T.53, L.54, E.78, S.89, F.90, R.218, I.239, T.240, D.241 Chain B: F.199, L.223, K.224, L.225, R.226, T.228, S.229, H.230, K.232 Ligands: MG.6, MG.7 17 PLIP interactions: 5 interactions with chain B, 12 interactions with chain A Hydrogen bonds: B:L.225, B:H.230, B:K.232, A:G.49, A:G.51, A:T.53, A:T.53, A:L.54, A:S.89, A:R.218, A:R.218, A:D.241, A:D.241 Salt bridges: B:K.224, B:R.226, A:K.52, A:K.52 ATP.8: 21 residues within 4Å: Chain B: T.290, G.291, T.292, G.293, K.294, T.295, L.296, E.318, S.330, W.331, R.451, I.472 Chain C: K.457, M.458, R.459, S.461, W.462, H.463, K.465 Ligands: MG.10, MG.11 21 PLIP interactions: 15 interactions with chain B, 6 interactions with chain C Hydrogen bonds: B:G.291, B:G.293, B:K.294, B:T.295, B:L.296, B:R.451, B:D.474, B:D.474, C:E.432, C:M.458, C:H.463, C:K.465 Water bridges: B:T.295, B:T.295, B:T.295, B:T.415, B:T.415 Salt bridges: B:K.294, B:K.294, C:K.457, C:R.459 ATP.9: 20 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 Chain C: K.224, L.225, R.226, G.227, T.228, S.229, H.230 Ligands: MG.12 21 PLIP interactions: 17 interactions with chain B, 4 interactions with chain C Hydrogen bonds: B:G.49, B:G.49, B:T.50, B:T.50, B:G.51, B:T.53, B:T.53, B:T.53, B:L.54, B:E.78, B:S.89, B:R.218, B:R.218, B:D.241, B:D.241, C:L.225, C:H.230 Salt bridges: B:K.52, B:K.52, C:K.224, C:R.226 ATP.13: 23 residues within 4Å: Chain C: 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.15, MG.16 16 PLIP interactions: 12 interactions with chain C, 4 interactions with chain D Hydrogen bonds: C:T.290, C:G.291, C:G.293, C:K.294, C:T.295, C:T.295, C:L.296, C:R.451, C:D.474, C:D.474, D:M.458, D:H.463 Salt bridges: C:K.294, C:K.294, D:K.457, D:R.459 ATP.14: 23 residues within 4Å: Chain C: S.48, G.49, T.50, G.51, K.52, T.53, L.54, S.89, F.90, I.239, T.240, D.241 Chain D: L.223, K.224, L.225, R.226, G.227, T.228, S.229, H.230, K.232 Ligands: MG.17, MG.18 17 PLIP interactions: 5 interactions with chain D, 12 interactions with chain C Hydrogen bonds: D:L.225, D:H.230, D:K.232, C:G.49, C:G.51, C:K.52, C:T.53, C:T.53, C:S.89, C:R.218, C:D.241, C:D.241 Salt bridges: D:K.224, D:R.226, C:K.52, C:K.52 Water bridges: C:N.86 ATP.19: 23 residues within 4Å: Chain D: T.290, G.291, T.292, G.293, K.294, T.295, L.296, E.318, S.330, W.331, R.451, I.472, S.473 Chain E: K.457, M.458, R.459, G.460, S.461, W.462, H.463, K.465 Ligands: MG.21, MG.22 16 PLIP interactions: 11 interactions with chain D, 5 interactions with chain E Hydrogen bonds: D:T.290, D:G.291, D:G.291, D:G.293, D:K.294, D:T.295, D:L.296, D:R.451, D:R.451, E:G.460, E:H.463, E:K.465 Salt bridges: D:K.294, D:K.294, E:K.457, E:R.459 ATP.20: 23 residues within 4Å: Chain D: S.48, G.49, T.50, G.51, K.52, T.53, L.54, E.78, S.89, F.90, I.239, T.240, D.241 Chain E: K.224, L.225, R.226, G.227, T.228, S.229, H.230, K.232 Ligands: MG.23, MG.24 23 PLIP interactions: 7 interactions with chain E, 16 interactions with chain D Hydrogen bonds: E:L.225, E:H.230, E:K.232, D:G.49, D:T.50, D:T.50, D:G.51, D:K.52, D:T.53, D:T.53, D:L.54, D:E.78, D:E.78, D:S.89, D:S.89, D:D.241 Water bridges: E:G.227, D:K.52 Salt bridges: E:K.224, E:K.224, E:R.226, D:K.52, D:K.52 ATP.26: 21 residues within 4Å: Chain E: T.290, G.291, T.292, G.293, K.294, T.295, L.296, S.330, W.331, I.472, S.473 Chain F: F.456, K.457, M.458, R.459, G.460, S.461, W.462, H.463, K.465 Ligands: MG.28 21 PLIP interactions: 13 interactions with chain E, 8 interactions with chain F Hydrogen bonds: E:T.290, E:T.290, E:G.291, E:G.293, E:K.294, E:T.295, E:T.295, E:L.296, E:S.330, 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 pi-Cation interactions: E:R.451 Water bridges: F:R.459, F:R.459, F:R.459 ATP.27: 22 residues within 4Å: Chain E: S.48, G.49, T.50, G.51, K.52, T.53, L.54, E.78, S.89, F.90, I.239, D.241 Chain F: L.223, K.224, L.225, R.226, T.228, S.229, H.230, K.232 Ligands: MG.25, MG.29 17 PLIP interactions: 11 interactions with chain E, 6 interactions with chain F Hydrogen bonds: E:G.49, E:T.50, E:G.51, E:K.52, E:T.53, E:L.54, E:S.89, E:D.241, E:D.241, F:L.225, F:H.230, F:K.232 Salt bridges: E:K.52, E:K.52, F:K.224, F:K.224, F:R.226 ATP.30: 22 residues within 4Å: Chain A: K.457, M.458, R.459, S.461, W.462, H.463, K.465 Chain F: T.290, G.291, T.292, G.293, K.294, T.295, L.296, E.318, W.331, R.451, I.472, S.473, D.474 Ligands: MG.4, MG.34 17 PLIP interactions: 12 interactions with chain F, 5 interactions with chain A Hydrogen bonds: F:G.291, F:G.293, F:K.294, F:T.295, F:T.295, F:T.295, F:L.296, F:R.451, F:D.474, 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.31: 23 residues within 4Å: Chain A: F.199, L.223, K.224, R.226, G.227, 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.32, MG.33 15 PLIP interactions: 11 interactions with chain F, 4 interactions with chain A Hydrogen bonds: F:G.49, F:G.49, F:T.50, F:G.51, F:T.53, F:L.54, F:S.89, F:D.241, F:D.241, A:H.230, A:K.232 Salt bridges: F:K.52, F:K.52, A:K.224, A:R.226

22 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 5 residues within 4Å: Chain A: T.295, E.318, E.319 Chain B: R.459 Ligands: ATP.1 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:T.295, H2O.1, H2O.1, H2O.1 MG.4: 6 residues within 4Å: Chain A: E.432, K.457, R.459 Chain F: T.290, E.318 Ligands: ATP.30 No protein-ligand interaction detected (PLIP) MG.5: 5 residues within 4Å: Chain A: T.290, K.294, T.415 Chain B: K.457 Ligands: ATP.1 No protein-ligand interaction detected (PLIP) MG.6: 6 residues within 4Å: Chain A: K.52, T.53, D.145, T.181 Ligands: ATP.2, MG.7 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.53 MG.7: 6 residues within 4Å: Chain A: K.52 Chain B: F.199, K.224, R.226 Ligands: ATP.2, MG.6 No protein-ligand interaction detected (PLIP) MG.10: 4 residues within 4Å: Chain B: T.295, E.318, D.378 Ligands: ATP.8 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:T.295, H2O.1, H2O.1, H2O.1 MG.11: 4 residues within 4Å: Chain B: T.290, K.294, T.415 Ligands: ATP.8 No protein-ligand interaction detected (PLIP) MG.12: 5 residues within 4Å: Chain B: K.52, T.53, D.145, T.181 Ligands: ATP.9 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:T.53, B:D.145 MG.15: 4 residues within 4Å: Chain C: T.295, E.318, D.378 Ligands: ATP.13 4 PLIP interactions: 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:T.295, H2O.2, H2O.2, H2O.2 MG.16: 5 residues within 4Å: Chain C: T.290, E.318, T.415 Chain D: E.432 Ligands: ATP.13 No protein-ligand interaction detected (PLIP) MG.17: 5 residues within 4Å: Chain C: T.53, E.78, D.145 Ligands: ATP.14, MG.18 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.53 MG.18: 5 residues within 4Å: Chain C: T.53, E.78 Chain D: R.226 Ligands: ATP.14, MG.17 No protein-ligand interaction detected (PLIP) MG.21: 4 residues within 4Å: Chain D: T.290, K.294, T.415 Ligands: ATP.19 No protein-ligand interaction detected (PLIP) MG.22: 4 residues within 4Å: Chain D: T.295, E.318, E.319 Ligands: ATP.19 4 PLIP interactions: 1 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:T.295, H2O.3, H2O.3, H2O.3 MG.23: 6 residues within 4Å: Chain D: K.52, T.53, D.145, S.146 Ligands: ATP.20, MG.24 3 PLIP interactions: 1 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:T.53, H2O.3, H2O.4 MG.24: 5 residues within 4Å: Chain D: K.52, E.183 Chain E: F.199 Ligands: ATP.20, MG.23 No protein-ligand interaction detected (PLIP) MG.25: 6 residues within 4Å: Chain E: S.48, G.49, K.52 Chain F: F.199, K.224 Ligands: ATP.27 No protein-ligand interaction detected (PLIP) MG.28: 3 residues within 4Å: Chain E: T.295, D.378 Ligands: ATP.26 4 PLIP interactions: 1 interactions with chain E, 3 Ligand-Water interactions Metal complexes: E:T.295, H2O.4, H2O.4, H2O.4 MG.29: 3 residues within 4Å: Chain E: T.53, D.145 Ligands: ATP.27 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:T.53 MG.32: 4 residues within 4Å: Chain F: T.53, E.78, D.145 Ligands: ATP.31 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:T.53 MG.33: 4 residues within 4Å: Chain A: K.224 Chain F: S.48, G.49 Ligands: ATP.31 No protein-ligand interaction detected (PLIP) MG.34: 5 residues within 4Å: Chain A: R.459 Chain F: T.295, E.318, E.319 Ligands: ATP.30 3 PLIP interactions: 2 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:T.295, F:E.318, H2O.4

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pattanayek, R. et al., Structures of KaiC Circadian Clock Mutant Proteins: A New Phosphorylation Site at T426 and Mechanisms of Kinase, ATPase and Phosphatase. Plos One (2009)

Release Date

2010-03-31

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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