SMTL ID : 1u9i.1

Crystal Structure of Circadian Clock Protein KaiC with Phosphorylation Sites

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-hexamer

Ligands

6 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain A: T.295, E.318, E.319, D.378 Ligands: ATP.2 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:T.295, A:E.319 MG.4: 4 residues within 4Å: Chain B: T.295, E.318, D.378 Ligands: ATP.5 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:T.295, B:E.318, B:D.378 MG.7: 4 residues within 4Å: Chain C: T.295, E.318, E.319 Ligands: ATP.8 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.295 MG.10: 5 residues within 4Å: Chain D: T.295, E.318, E.319, D.378 Ligands: ATP.11 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.295 MG.13: 5 residues within 4Å: Chain E: T.295, E.318, E.319, D.378 Ligands: ATP.14 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:T.295, E:E.319 MG.16: 5 residues within 4Å: Chain F: T.295, E.318, E.319, D.378 Ligands: ATP.17 3 PLIP interactions: 2 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:T.295, F:E.318, H2O.3

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

ATP.2: 21 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, D.474 Chain B: K.457, M.458, R.459, G.460, S.461, W.462, H.463, K.465 Ligands: MG.1 16 PLIP interactions: 12 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:A.289, A:G.291, A:G.293, A:K.294, A:T.295, A:T.295, A:L.296, A:R.451, A:D.474, A:D.474, B:M.458, B:H.463 Salt bridges: A:K.294, A:K.294, B:K.457, B:R.459 ATP.3: 23 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: L.223, K.224, L.225, R.226, G.227, T.228, S.229, H.230, K.232 21 PLIP interactions: 16 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:G.49, A:G.49, A:T.50, A:G.51, A:K.52, A:T.53, A:T.53, A:T.53, A:L.54, A:E.78, A:S.89, A:R.218, A:D.241, A:D.241, B:L.225, B:H.230, B:K.232 Salt bridges: A:K.52, A:K.52, B:K.224, B:R.226 ATP.5: 23 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, S.473, D.474 Chain C: K.457, M.458, R.459, G.460, S.461, W.462, H.463, K.465 Ligands: MG.4 17 PLIP interactions: 4 interactions with chain C, 13 interactions with chain B Hydrogen bonds: C:M.458, C:H.463, B:T.290, B:G.291, B:G.293, B:K.294, B:T.295, B:T.295, B:T.295, B:L.296, B:R.451, B:D.474, B:D.474 Salt bridges: C:K.457, C:R.459, B:K.294, B:K.294 ATP.6: 21 residues within 4Å: Chain B: 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 C: L.223, K.224, L.225, R.226, G.227, T.228, S.229, H.230, K.232 22 PLIP interactions: 17 interactions with chain B, 5 interactions with chain C Hydrogen bonds: B:G.49, B:G.49, B:T.50, B:T.50, B:G.51, B:K.52, B:T.53, B:T.53, B:T.53, B:L.54, B:E.78, B:E.78, B:S.89, 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:R.226 ATP.8: 22 residues within 4Å: Chain C: 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, D.474 Chain D: K.457, M.458, R.459, S.461, W.462, H.463, K.465 Ligands: MG.7 15 PLIP interactions: 11 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: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.9: 24 residues within 4Å: Chain C: 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 D: F.199, L.223, K.224, L.225, R.226, G.227, T.228, S.229, H.230, K.232 24 PLIP interactions: 6 interactions with chain D, 18 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:T.53, C:L.54, C:E.78, C:E.78, C:S.89, C:S.89, C:R.218, C:D.241 Salt bridges: D:K.224, D:K.224, D:R.226, C:K.52, C:K.52 ATP.11: 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, D.474 Chain E: K.457, M.458, R.459, G.460, S.461, W.462, H.463, K.465 Ligands: MG.10 17 PLIP interactions: 12 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:D.474, D:D.474, E:M.458, E:H.463, E:K.465 Salt bridges: D:K.294, D:K.294, E:K.457, E:R.459 ATP.12: 22 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: L.223, K.224, L.225, R.226, G.227, T.228, S.229, H.230, K.232 23 PLIP interactions: 5 interactions with chain E, 18 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:T.50, D:G.51, D:K.52, D:T.53, D:T.53, D:T.53, D:L.54, D:E.78, D:E.78, D:S.89, D:R.218, D:D.241, D:D.241 Salt bridges: E:K.224, E:R.226, D:K.52, D:K.52 ATP.14: 22 residues within 4Å: Chain E: 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, D.474 Chain F: K.457, M.458, R.459, S.461, W.462, H.463, K.465 Ligands: MG.13 15 PLIP interactions: 11 interactions with chain E, 4 interactions with chain F Hydrogen bonds: E:G.291, E:G.293, E:K.294, E:T.295, E:T.295, E:L.296, E:R.451, E:D.474, E:D.474, F:M.458, F:H.463 Salt bridges: E:K.294, E:K.294, F:K.457, F:R.459 ATP.15: 23 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, T.240, D.241 Chain F: F.199, L.223, K.224, L.225, R.226, G.227, T.228, S.229, H.230, K.232 22 PLIP interactions: 6 interactions with chain F, 16 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:T.53, E:T.53, E:L.54, E:E.78, E:S.89, E:S.89, E:R.218, E:D.241 Water bridges: F:G.227 Salt bridges: F:K.224, F:R.226, E:K.52, E:K.52 ATP.17: 23 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, E.318, S.330, W.331, R.451, I.472, S.473, D.474 Ligands: MG.16 15 PLIP interactions: 11 interactions with chain F, 4 interactions with chain A Hydrogen bonds: F:G.291, F:G.293, F:K.294, F:T.295, F:T.295, F:L.296, F:R.451, F:D.474, F:D.474, A:M.458, A:H.463 Salt bridges: F:K.294, F:K.294, A:K.457, A:R.459 ATP.18: 22 residues within 4Å: Chain A: L.223, K.224, L.225, R.226, T.228, S.229, H.230, K.232 Chain F: 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 21 PLIP interactions: 5 interactions with chain A, 16 interactions with chain F Hydrogen bonds: A:H.230, A:K.232, F:G.49, F:G.49, F:T.50, F:G.51, F:K.52, F:T.53, F:T.53, F:T.53, F:L.54, F:E.78, F:S.89, F:R.218, F:D.241, F:D.241 Salt bridges: A:K.224, A:K.224, A:R.226, F:K.52, F:K.52

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xu, Y. et al., Identification of key phosphorylation sites in the circadian clock protein KaiC by crystallographic and mutagenetic analyses. PROC.NATL.ACAD.SCI.USA (2004)

Release Date

2005-04-19

Peptides

KaiC: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

KaiC

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