SMTL ID : 4o0m.1

Crystal structure of T. Elongatus BP-1 Clock Protein KaiC

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.84 Å

Oligo State

homo-hexamer

Ligands

12 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: T.295, E.318, E.319 Ligands: ATP.2 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.295 MG.4: 4 residues within 4Å: Chain A: T.54, E.79, D.146 Ligands: ATP.3 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:T.54, A:E.79 MG.5: 5 residues within 4Å: Chain B: T.295, E.318, E.319, D.378 Ligands: ATP.6 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.295 MG.7: 4 residues within 4Å: Chain B: T.54, E.79, D.146 Ligands: ATP.8 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.54 MG.9: 2 residues within 4Å: Chain C: T.295 Ligands: ATP.10 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.295 MG.12: 3 residues within 4Å: Chain C: T.54, D.146 Ligands: ATP.11 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.54 MG.13: 4 residues within 4Å: Chain D: T.295, E.318, E.319 Ligands: ATP.14 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.295 MG.16: 4 residues within 4Å: Chain D: T.54, E.79, D.146 Ligands: ATP.15 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:T.54, D:E.79 MG.17: 5 residues within 4Å: Chain E: T.295, E.318, E.319, D.378 Ligands: ATP.18 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:T.295 MG.19: 4 residues within 4Å: Chain E: T.54, E.79, D.146 Ligands: ATP.20 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:T.54 MG.21: 2 residues within 4Å: Chain F: T.295 Ligands: ATP.22 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:T.295 MG.24: 3 residues within 4Å: Chain F: T.54, D.146 Ligands: ATP.23 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:T.54

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

ATP.2: 19 residues within 4Å: Chain A: 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 B: K.457, M.458, R.459, S.461, W.462, H.463 Ligands: MG.1 15 PLIP interactions: 11 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:T.290, A:T.290, A:G.291, A:T.292, A:G.293, A:K.294, A:T.295, A:L.296, A:R.451, B:M.458, B:H.463 Salt bridges: A:K.294, A:K.294, B:K.457, B:R.459 ATP.3: 21 residues within 4Å: Chain A: G.50, T.51, G.52, K.53, T.54, L.55, E.79, S.90, F.91, I.240 Chain B: F.200, L.224, K.225, L.226, R.227, G.228, T.229, T.230, H.231, K.233 Ligands: MG.4 22 PLIP interactions: 14 interactions with chain A, 8 interactions with chain B Hydrogen bonds: A:G.50, A:G.50, A:T.51, A:G.52, A:K.53, A:T.54, A:T.54, A:T.54, A:L.55, A:S.90, A:S.90, A:R.219, B:F.200, B:L.226, B:H.231, B:K.233 Salt bridges: A:K.53, A:K.53, B:K.225, B:K.225, B:R.227 Water bridges: B:G.228 ATP.6: 21 residues within 4Å: Chain B: T.290, G.291, T.292, G.293, K.294, T.295, L.296, E.318, W.331, T.415, R.451, I.472, T.473 Chain C: K.457, M.458, R.459, G.460, S.461, W.462, H.463 Ligands: MG.5 17 PLIP interactions: 4 interactions with chain C, 13 interactions with chain B Hydrogen bonds: C:M.458, C:H.463, B:G.291, B:G.291, B:T.292, B:G.293, B:K.294, B:T.295, B:L.296, B:E.318, B:T.415, B:R.451, B:R.451 Salt bridges: C:K.457, C:R.459, B:K.294, B:K.294 ATP.8: 23 residues within 4Å: Chain B: T.48, S.49, G.50, T.51, G.52, K.53, T.54, L.55, S.90, F.91, R.219, I.240 Chain C: F.200, L.224, K.225, L.226, R.227, G.228, T.229, T.230, H.231, K.233 Ligands: MG.7 17 PLIP interactions: 11 interactions with chain B, 6 interactions with chain C Hydrogen bonds: B:G.50, B:T.51, B:G.52, B:K.53, B:T.54, B:L.55, B:S.90, B:S.90, B:R.219, C:F.200, C:L.226, C:H.231, C:K.233 Salt bridges: B:K.53, B:K.53, C:K.225, C:R.227 ATP.10: 21 residues within 4Å: Chain C: T.290, G.291, T.292, G.293, K.294, T.295, L.296, W.331, T.415, R.451, I.472, T.473 Chain D: T.432, K.457, M.458, R.459, S.461, W.462, H.463, K.465 Ligands: MG.9 17 PLIP interactions: 11 interactions with chain C, 6 interactions with chain D Hydrogen bonds: C:G.291, C:T.292, C:T.292, C:G.293, C:K.294, C:T.295, C:L.296, C:T.415, C:R.451, D:M.458, D:S.461, D:H.463, D:K.465 Salt bridges: C:K.294, C:K.294, D:K.457, D:R.459 ATP.11: 21 residues within 4Å: Chain C: T.48, S.49, G.50, T.51, G.52, K.53, T.54, L.55, S.90, F.91, R.219, I.240 Chain D: F.200, L.224, K.225, L.226, R.227, T.229, T.230, H.231 Ligands: MG.12 20 PLIP interactions: 14 interactions with chain C, 6 interactions with chain D Hydrogen bonds: C:G.50, C:G.50, C:T.51, C:G.52, C:K.53, C:T.54, C:T.54, C:L.55, C:S.90, C:S.90, C:R.219, C:R.219, D:F.200, D:H.231 Salt bridges: C:K.53, C:K.53, D:K.225, D:K.225, D:R.227 Water bridges: D:G.228 ATP.14: 19 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, S.461, W.462, H.463 Ligands: MG.13 14 PLIP interactions: 10 interactions with chain D, 4 interactions with chain E Hydrogen bonds: D:T.290, D:G.291, D:T.292, D:G.293, D:K.294, D:T.295, D:L.296, D:R.451, E:M.458, E:H.463 Salt bridges: D:K.294, D:K.294, E:K.457, E:R.459 ATP.15: 21 residues within 4Å: Chain D: G.50, T.51, G.52, K.53, T.54, L.55, E.79, S.90, F.91, I.240 Chain E: F.200, L.224, K.225, L.226, R.227, G.228, T.229, T.230, H.231, K.233 Ligands: MG.16 23 PLIP interactions: 8 interactions with chain E, 15 interactions with chain D Hydrogen bonds: E:F.200, E:L.226, E:H.231, E:K.233, D:G.50, D:G.50, D:T.51, D:G.52, D:K.53, D:T.54, D:T.54, D:T.54, D:L.55, D:E.79, D:S.90, D:S.90, D:R.219 Water bridges: E:G.228 Salt bridges: E:K.225, E:K.225, E:R.227, D:K.53, D:K.53 ATP.18: 21 residues within 4Å: Chain E: T.290, G.291, T.292, G.293, K.294, T.295, L.296, E.318, W.331, T.415, R.451, I.472, T.473 Chain F: K.457, M.458, R.459, G.460, S.461, W.462, H.463 Ligands: MG.17 18 PLIP interactions: 14 interactions with chain E, 4 interactions with chain F Hydrogen bonds: E:T.290, E:G.291, E:G.291, E:T.292, E:T.292, E:G.293, E:K.294, E:T.295, E:L.296, E:E.318, E:R.451, E:R.451, F:M.458, F:H.463 Salt bridges: E:K.294, E:K.294, F:K.457, F:R.459 ATP.20: 23 residues within 4Å: Chain E: T.48, S.49, G.50, T.51, G.52, K.53, T.54, L.55, S.90, F.91, R.219, I.240 Chain F: F.200, L.224, K.225, L.226, R.227, G.228, T.229, T.230, H.231, K.233 Ligands: MG.19 18 PLIP interactions: 6 interactions with chain F, 12 interactions with chain E Hydrogen bonds: F:F.200, F:L.226, F:H.231, F:K.233, E:G.50, E:T.51, E:T.51, E:G.52, E:K.53, E:T.54, E:L.55, E:S.90, E:S.90, E:R.219 Salt bridges: F:K.225, F:R.227, E:K.53, E:K.53 ATP.22: 21 residues within 4Å: Chain A: T.432, 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, W.331, T.415, R.451, I.472, T.473 Ligands: MG.21 15 PLIP interactions: 9 interactions with chain F, 6 interactions with chain A Hydrogen bonds: F:G.291, F:T.292, F:G.293, F:K.294, F:T.295, F:L.296, F:R.451, A:M.458, A:S.461, A:H.463, A:K.465 Salt bridges: F:K.294, F:K.294, A:K.457, A:R.459 ATP.23: 21 residues within 4Å: Chain A: F.200, L.224, K.225, L.226, R.227, T.229, T.230, H.231 Chain F: T.48, S.49, G.50, T.51, G.52, K.53, T.54, L.55, S.90, F.91, R.219, I.240 Ligands: MG.24 21 PLIP interactions: 6 interactions with chain A, 15 interactions with chain F Hydrogen bonds: A:F.200, A:H.231, F:G.50, F:G.50, F:T.51, F:T.51, F:G.52, F:K.53, F:T.54, F:T.54, F:L.55, F:S.90, F:S.90, F:R.219, F:R.219 Water bridges: A:G.228 Salt bridges: A:K.225, A:K.225, A:R.227, F:K.53, F:K.53

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pattanayek, R. et al., An arginine tetrad as mediator of input-dependent and input-independent ATPases in the clock protein KaiC. Acta Crystallogr.,Sect.D (2014)

Release Date

2014-05-14

Peptides

Circadian clock protein kinase 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 kinase KaiC