SMTL ID : 3s1a.1

Crystal structure of the phosphorylation-site double mutant S431E/T432E of the KaiC circadian clock protein

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

homo-hexamer

Ligands

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

ATP.1: 24 residues within 4Å: Chain A: T.290, G.291, T.292, G.293, K.294, T.295, L.296, N.327, S.330, W.331, R.451, I.472, S.473, D.474 Chain B: K.457, M.458, R.459, G.460, S.461, W.462, H.463, K.465 Ligands: MG.3, MG.4 16 PLIP interactions: 12 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:G.291, A:G.293, A:K.294, A:T.295, A:T.295, A:L.296, A:N.327, 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.2: 23 residues within 4Å: Chain A: 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, T.228, S.229, H.230, K.232 Ligands: MG.5, MG.7 20 PLIP interactions: 14 interactions with chain A, 6 interactions with chain B Hydrogen bonds: A:G.49, A:G.51, A:K.52, A:T.53, A:T.53, A:L.54, A:E.78, A:S.89, A:R.218, 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:K.224, B:R.226 ATP.8: 23 residues within 4Å: Chain B: 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 Chain C: K.457, M.458, R.459, G.460, S.461, W.462, H.463, K.465 Ligands: MG.10, MG.11 17 PLIP interactions: 12 interactions with chain B, 5 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:M.458, C:H.463, C:K.465 Water bridges: B:K.294, B:K.294 Salt bridges: B:K.294, B:K.294, C:K.457, C:R.459 ATP.9: 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: 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 C, 14 interactions with chain B Hydrogen bonds: C:L.225, C:H.230, C:K.232, B:G.49, B:G.51, B:T.53, B:T.53, B:L.54, B:E.78, B:E.78, B:S.89, B:D.241, B:D.241 Salt bridges: C:K.224, C:K.224, C:R.226, B:K.52, B:K.52 Water bridges: B:R.218, B:R.218 ATP.13: 24 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, G.460, S.461, W.462, H.463, K.465 Ligands: MG.15, MG.16 17 PLIP interactions: 13 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: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: 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, I.239, T.240, D.241 Chain D: F.199, K.224, L.225, R.226, G.227, T.228, S.229, H.230, K.232 Ligands: MG.17, MG.18 20 PLIP interactions: 15 interactions with chain C, 5 interactions with chain D Hydrogen bonds: 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:S.89, C:D.241, C:D.241, D:L.225, D:H.230, D:K.232 Salt bridges: C:K.52, C:K.52, D:K.224, D:R.226 ATP.19: 22 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 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, E:M.458, E:G.460, E:H.463 Water bridges: D:E.319 Salt bridges: D:K.294, D:K.294, E:K.457, E:R.459 ATP.20: 24 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, R.218, I.239, T.240, D.241 Chain E: F.199, K.224, L.225, R.226, T.228, S.229, H.230, K.232 Ligands: MG.23, MG.24 21 PLIP interactions: 16 interactions with chain D, 5 interactions with chain E Hydrogen bonds: 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:R.218, D:D.241, D:D.241, E:L.225, E:H.230, E:K.232 Salt bridges: D:K.52, D:K.52, E:K.224, E:R.226 ATP.25: 23 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.27, MG.28 16 PLIP interactions: 5 interactions with chain F, 11 interactions with chain E Hydrogen bonds: F:M.458, F:H.463, F:K.465, E:T.290, E:G.291, E:G.293, E:K.294, E:T.295, E:L.296, E:R.451, E:D.474, E:D.474 Salt bridges: F:K.457, F:R.459, E:K.294, E:K.294 ATP.26: 21 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, D.145, I.239, T.240, D.241 Chain F: K.224, L.225, R.226, T.228, S.229, H.230, K.232 21 PLIP interactions: 15 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:T.53, E:L.54, E:E.78, E:S.89, E:R.218, E:D.241, E:D.241, F:L.225, F:H.230, F:K.232 Water bridges: E:R.218 Salt bridges: E:K.52, E:K.52, F:K.224, F:K.224, F:R.226 ATP.29: 24 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.6, MG.33 18 PLIP interactions: 5 interactions with chain A, 13 interactions with chain F Hydrogen bonds: A:M.458, A:H.463, A:K.465, 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 Salt bridges: A:K.457, A:R.459, F:K.294, F:K.294 Water bridges: F:D.474 ATP.30: 23 residues within 4Å: Chain A: F.199, 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.31, MG.32 18 PLIP interactions: 6 interactions with chain A, 12 interactions with chain F Hydrogen bonds: A:L.225, A:H.230, A:K.232, F:G.49, F:T.50, F:G.51, F:K.52, F:T.53, F:T.53, F:L.54, F:S.89, F:D.241, F:D.241 Salt bridges: A:K.224, A:K.224, A:R.226, F:K.52, F:K.52

21 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 5 residues within 4Å: Chain A: T.295, E.319, D.378 Chain B: R.459 Ligands: ATP.1 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:T.295, A:E.319, H2O.1 MG.4: 5 residues within 4Å: Chain A: T.290, K.294, T.415 Chain B: E.432 Ligands: ATP.1 No protein-ligand interaction detected (PLIP) MG.5: 4 residues within 4Å: Chain A: T.53, D.145, T.181 Ligands: ATP.2 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.53 MG.6: 6 residues within 4Å: Chain A: E.431, E.432, K.457, R.459 Chain F: T.290 Ligands: ATP.29 No protein-ligand interaction detected (PLIP) MG.7: 5 residues within 4Å: Chain A: S.48 Chain B: E.198, F.199, K.224 Ligands: ATP.2 No protein-ligand interaction detected (PLIP) MG.10: 5 residues within 4Å: Chain B: T.295, E.318, E.319, D.378 Ligands: ATP.8 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:T.295, B:E.318, H2O.1, H2O.1, H2O.1 MG.11: 5 residues within 4Å: Chain B: T.290, K.294, T.415 Chain C: E.432 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: 5 residues within 4Å: Chain C: T.290, K.294, T.415 Chain D: E.432 Ligands: ATP.13 No protein-ligand interaction detected (PLIP) MG.16: 6 residues within 4Å: Chain C: T.295, E.318, E.319, D.378 Chain D: R.459 Ligands: ATP.13 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:T.295, C:E.319, H2O.1, H2O.1 MG.17: 4 residues within 4Å: Chain C: T.53, 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 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:T.53, C:E.78 MG.21: 4 residues within 4Å: Chain D: T.295, E.318, E.319 Ligands: ATP.19 3 PLIP interactions: 1 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:T.295, H2O.1, H2O.1 MG.22: 5 residues within 4Å: Chain D: T.290, K.294, T.415 Chain E: E.432 Ligands: ATP.19 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.415 MG.23: 4 residues within 4Å: Chain D: S.48, K.52 Chain E: F.199 Ligands: ATP.20 No protein-ligand interaction detected (PLIP) MG.24: 4 residues within 4Å: Chain D: K.52, T.53, D.145 Ligands: ATP.20 3 PLIP interactions: 1 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:T.53, H2O.1, H2O.1 MG.27: 5 residues within 4Å: Chain E: T.295, E.318, E.319, D.378 Ligands: ATP.25 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:T.295 MG.28: 6 residues within 4Å: Chain E: T.290, E.318, T.415 Chain F: E.432, K.457 Ligands: ATP.25 No protein-ligand interaction detected (PLIP) MG.31: 3 residues within 4Å: Chain F: T.53, D.145 Ligands: ATP.30 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:T.53 MG.32: 6 residues within 4Å: Chain A: F.199, K.224 Chain F: S.48, G.49, K.52 Ligands: ATP.30 No protein-ligand interaction detected (PLIP) MG.33: 6 residues within 4Å: Chain A: R.459 Chain F: T.295, E.318, E.319, D.378 Ligands: ATP.29 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:T.295, F:E.318

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pattanayek, R. et al., Combined SAXS/EM Based Models of the S. elongatus Post-Translational Circadian Oscillator and its Interactions with the Output His-Kinase SasA. Plos One (2011)

Release Date

2011-09-21

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