SMTL ID : 4ijm.1

Crystal structure of circadian clock protein KaiC A422V mutant

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.35 Å

Oligo State

homo-hexamer

Ligands

7 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: T.282, E.306 Ligands: ATP.2, MG.10 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:T.282, A:E.306, H2O.1, H2O.2 MG.5: 4 residues within 4Å: Chain B: T.282, E.305, D.365 Ligands: ATP.6 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:T.282, B:E.305, H2O.4 MG.10: 3 residues within 4Å: Chain B: R.446 Ligands: MG.1, ATP.2 No protein-ligand interaction detected (PLIP) MG.11: 5 residues within 4Å: Chain C: T.282, E.305, E.306, D.365 Ligands: ATP.12 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:T.282, C:E.305 MG.15: 3 residues within 4Å: Chain D: T.282, E.306 Ligands: ATP.16 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:T.282, D:E.306, H2O.10 MG.19: 5 residues within 4Å: Chain E: T.282, E.305, E.306, D.365 Ligands: ATP.20 3 PLIP interactions: 2 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:T.282, E:E.305, H2O.12 MG.24: 5 residues within 4Å: Chain F: T.282, E.305, E.306, D.365 Ligands: ATP.25 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:T.282, F:E.305

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

ATP.2: 25 residues within 4Å: Chain A: T.277, G.278, T.279, G.280, K.281, T.282, L.283, E.305, E.306, W.318, Y.429, R.438, I.459, S.460, D.461 Chain B: K.444, M.445, R.446, G.447, S.448, W.449, H.450, K.452 Ligands: MG.1, MG.10 20 PLIP interactions: 15 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:G.278, A:G.280, A:K.281, A:T.282, A:T.282, A:T.282, A:L.283, A:Y.429, A:Y.429, A:R.438, A:R.438, A:D.461, A:D.461, B:M.445, B:H.450, B:K.452 Salt bridges: A:K.281, A:K.281, B:K.444, B:R.446 ATP.3: 20 residues within 4Å: Chain A: S.35, G.36, T.37, G.38, K.39, T.40, L.41, S.76, F.77, R.205, I.226, T.227, D.228 Chain B: L.210, K.211, R.213, T.215, S.216, H.217, K.219 19 PLIP interactions: 5 interactions with chain B, 14 interactions with chain A Hydrogen bonds: B:L.212, B:H.217, A:G.36, A:G.36, A:T.37, A:G.38, A:K.39, A:T.40, A:T.40, A:L.41, A:S.76, A:R.205, A:R.205, A:D.228 Salt bridges: B:K.211, B:K.211, B:R.213, A:K.39, A:K.39 ATP.4: 22 residues within 4Å: Chain A: F.186, L.210, K.211, L.212, R.213, T.215, S.216, H.217, K.219 Chain F: T.34, S.35, G.36, T.37, G.38, K.39, T.40, L.41, S.76, F.77, I.226, T.227, D.228 21 PLIP interactions: 15 interactions with chain F, 6 interactions with chain A Hydrogen bonds: F:G.36, F:G.36, F:T.37, F:G.38, F:K.39, F:T.40, F:T.40, F:T.40, F:L.41, F:S.76, F:D.228, F:D.228, A:L.212, A:H.217, A:K.219 Water bridges: F:R.205 Salt bridges: F:K.39, F:K.39, A:K.211, A:K.211, A:R.213 ATP.6: 23 residues within 4Å: Chain B: T.277, G.278, T.279, G.280, K.281, T.282, L.283, E.305, S.317, W.318, R.438, I.459, S.460, D.461 Chain C: K.444, M.445, R.446, G.447, S.448, W.449, H.450, K.452 Ligands: MG.5 17 PLIP interactions: 13 interactions with chain B, 4 interactions with chain C Hydrogen bonds: B:G.278, B:G.278, B:G.280, B:K.281, B:T.282, B:T.282, B:L.283, B:T.402, B:R.438, B:D.461, B:D.461, C:M.445, C:H.450 Salt bridges: B:K.281, B:K.281, C:K.444, C:R.446 ATP.7: 20 residues within 4Å: Chain B: S.35, G.36, T.37, G.38, K.39, T.40, L.41, S.76, F.77, I.226, T.227, D.228 Chain C: L.210, K.211, L.212, R.213, T.215, S.216, H.217, K.219 19 PLIP interactions: 14 interactions with chain B, 5 interactions with chain C Hydrogen bonds: B:G.36, B:G.36, B:T.37, B:T.37, B:G.38, B:K.39, B:T.40, B:T.40, B:T.40, B:L.41, B:S.76, B:D.228, C:L.212, C:H.217, C:K.219 Salt bridges: B:K.39, B:K.39, C:K.211, C:R.213 ATP.12: 23 residues within 4Å: Chain C: T.277, G.278, T.279, G.280, K.281, T.282, L.283, E.305, S.317, W.318, R.438, I.459, D.461 Chain D: T.419, K.444, M.445, R.446, G.447, S.448, W.449, H.450, K.452 Ligands: MG.11 24 PLIP interactions: 19 interactions with chain C, 5 interactions with chain D Hydrogen bonds: C:T.277, C:T.277, C:G.278, C:G.278, C:T.279, C:T.279, C:G.280, C:K.281, C:T.282, C:T.282, C:L.283, C:R.438, C:R.438, C:D.461, C:D.461, D:M.445, D:R.446, D:H.450 Water bridges: C:K.281, C:T.402 Salt bridges: C:K.281, C:K.281, D:K.444, D:R.446 ATP.13: 23 residues within 4Å: Chain C: S.35, G.36, T.37, G.38, K.39, T.40, L.41, E.65, S.76, F.77, I.226, T.227, D.228 Chain D: F.186, L.210, K.211, L.212, R.213, G.214, T.215, S.216, H.217, K.219 25 PLIP interactions: 18 interactions with chain C, 7 interactions with chain D Hydrogen bonds: C:G.36, C:G.36, C:T.37, C:T.37, C:T.37, C:G.38, C:K.39, C:T.40, C:T.40, C:L.41, C:E.65, C:S.76, C:R.205, C:D.228, D:L.212, D:H.217, D:K.219 Water bridges: C:K.39, C:K.39, D:G.214 Salt bridges: C:K.39, C:K.39, D:K.211, D:K.211, D:R.213 ATP.16: 23 residues within 4Å: Chain D: T.277, G.278, T.279, G.280, K.281, T.282, L.283, E.305, E.306, S.317, W.318, R.438, I.459, S.460 Chain E: K.444, M.445, R.446, G.447, S.448, W.449, H.450, K.452 Ligands: MG.15 21 PLIP interactions: 16 interactions with chain D, 5 interactions with chain E Hydrogen bonds: D:T.277, D:G.278, D:G.278, D:T.279, D:T.279, D:G.280, D:K.281, D:T.282, D:T.282, D:T.282, D:L.283, D:E.305, D:R.438, D:R.438, E:M.445, E:G.447, E:H.450 Salt bridges: D:K.281, D:K.281, E:K.444, E:R.446 ATP.17: 21 residues within 4Å: Chain D: T.34, G.36, T.37, G.38, K.39, T.40, L.41, E.65, S.76, F.77, I.226, T.227, D.228 Chain E: L.210, K.211, L.212, R.213, T.215, S.216, H.217, K.219 20 PLIP interactions: 6 interactions with chain E, 14 interactions with chain D Hydrogen bonds: E:L.212, E:H.217, E:K.219, D:G.36, D:G.36, D:T.37, D:T.37, D:G.38, D:K.39, D:T.40, D:T.40, D:L.41, D:E.65, D:S.76, D:D.228 Salt bridges: E:K.211, E:K.211, E:R.213, D:K.39, D:K.39 ATP.20: 21 residues within 4Å: Chain E: T.277, G.278, T.279, G.280, K.281, T.282, L.283, E.305, S.317, W.318, R.438, I.459, S.460 Chain F: K.444, M.445, R.446, S.448, W.449, H.450, K.452 Ligands: MG.19 20 PLIP interactions: 7 interactions with chain F, 13 interactions with chain E Hydrogen bonds: F:M.445, F:G.447, F:H.450, E:T.277, E:T.277, E:G.278, E:G.278, E:G.280, E:K.281, E:T.282, E:T.282, E:L.283, E:R.438, E:R.438 Water bridges: F:R.446, F:R.446 Salt bridges: F:K.444, F:R.446, E:K.281, E:K.281 ATP.21: 22 residues within 4Å: Chain E: G.36, T.37, G.38, K.39, T.40, L.41, E.65, S.76, F.77, D.132, R.205, I.226, T.227, D.228 Chain F: L.210, K.211, L.212, R.213, T.215, S.216, H.217, K.219 19 PLIP interactions: 13 interactions with chain E, 6 interactions with chain F Hydrogen bonds: E:G.36, E:G.36, E:T.37, E:G.38, E:K.39, E:T.40, E:T.40, E:L.41, E:S.76, E:R.205, E:D.228, F:L.212, F:H.217, F:K.219 Salt bridges: E:K.39, E:K.39, F:K.211, F:K.211, F:R.213 ATP.25: 23 residues within 4Å: Chain A: K.444, M.445, R.446, G.447, S.448, W.449, H.450, K.452 Chain F: T.277, G.278, T.279, G.280, K.281, T.282, L.283, E.305, S.317, W.318, R.438, I.459, S.460, D.461 Ligands: MG.24 16 PLIP interactions: 4 interactions with chain A, 12 interactions with chain F Hydrogen bonds: A:M.445, A:H.450, F:G.278, F:G.278, F:G.280, F:K.281, F:T.282, F:L.283, F:R.438, F:R.438, F:D.461, F:D.461 Salt bridges: A:K.444, A:R.446, F:K.281, F:K.281

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

PO4.8: 4 residues within 4Å: Chain A: D.142, Y.181 Chain B: S.144, S.145 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:Q.139, A:Y.181, B:S.145, B:S.145 PO4.9: 5 residues within 4Å: Chain B: T.34, E.174, N.196, R.203 Chain C: I.178 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.34 Salt bridges: B:R.203 PO4.14: 7 residues within 4Å: Chain C: T.34, I.172, E.174, N.196, R.203 Chain D: I.178, L.210 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:T.34, C:E.174 Salt bridges: C:R.203 PO4.18: 6 residues within 4Å: Chain D: T.34, E.174, N.196, R.203 Chain E: I.178, L.210 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:T.34, D:E.174, D:E.174 Salt bridges: D:R.203 PO4.22: 7 residues within 4Å: Chain E: F.138, Q.139, Y.141, D.142, Y.181 Chain F: S.144, S.145 4 PLIP interactions: 2 interactions with chain F, 2 interactions with chain E Hydrogen bonds: F:S.145, F:S.145, E:F.138, E:D.142 PO4.23: 5 residues within 4Å: Chain E: T.34, E.174, R.203 Chain F: G.176, I.178 7 PLIP interactions: 7 interactions with chain E Hydrogen bonds: E:T.34, E:T.34, E:E.174 Water bridges: E:S.35, E:I.172, E:E.174 Salt bridges: E:R.203 PO4.26: 5 residues within 4Å: Chain A: I.178, L.210 Chain F: T.34, E.174, R.203 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:T.34, F:T.34, F:T.34 Salt bridges: F:R.203 PO4.27: 4 residues within 4Å: Chain A: K.219 Chain F: R.205, T.225, I.226 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain F Salt bridges: A:K.219, F:R.205 Hydrogen bonds: F:I.226

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Egli, M. et al., Loop-Loop Interactions Regulate KaiA-Stimulated KaiC Phosphorylation in the Cyanobacterial KaiABC Circadian Clock. Biochemistry (2013)

Release Date

2013-02-13

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