SMTL ID : 9ofh.1

Extended conformation of dusk state KaiC

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-hexamer

Ligands

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

ATP.1: 22 residues within 4Å: Chain A: S.56, G.57, T.58, G.59, K.60, T.61, L.62, E.86, S.97, F.98, R.226, I.247 Chain B: F.207, L.231, K.232, L.233, R.234, G.235, T.236, S.237, H.238 Ligands: MG.3 19 PLIP interactions: 6 interactions with chain B, 13 interactions with chain A Hydrogen bonds: B:E.206, B:L.233, B:G.235, B:H.238, A:G.57, A:G.57, A:T.58, A:G.59, A:K.60, A:T.61, A:T.61, A:L.62, A:S.97, A:S.97, A:R.226 Salt bridges: B:K.232, B:R.234, A:K.60, A:K.60 ATP.2: 23 residues within 4Å: Chain A: A.297, T.298, G.299, T.300, G.301, K.302, T.303, L.304, E.326, E.327, S.338, W.339, R.459, I.480, S.481 Chain B: K.465, M.466, R.467, G.468, S.469, W.470, H.471 Ligands: MG.4 19 PLIP interactions: 14 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:G.299, A:G.299, A:T.300, A:G.301, A:K.302, A:T.303, A:T.303, A:L.304, A:E.326, A:E.327, A:S.338, A:R.459, B:M.466, B:G.468, B:H.471 Salt bridges: A:K.302, A:K.302, B:K.465, B:R.467 ATP.5: 22 residues within 4Å: Chain B: S.56, G.57, T.58, G.59, K.60, T.61, L.62, E.86, S.97, F.98, R.226, I.247 Chain C: F.207, L.231, K.232, L.233, R.234, G.235, T.236, S.237, H.238 Ligands: MG.7 19 PLIP interactions: 13 interactions with chain B, 6 interactions with chain C Hydrogen bonds: B:G.57, B:G.57, B:T.58, B:G.59, B:K.60, B:T.61, B:T.61, B:L.62, B:S.97, B:S.97, B:R.226, C:E.206, C:L.233, C:G.235, C:H.238 Salt bridges: B:K.60, B:K.60, C:K.232, C:R.234 ATP.6: 23 residues within 4Å: Chain B: A.297, T.298, G.299, T.300, G.301, K.302, T.303, L.304, E.326, E.327, S.338, W.339, R.459, I.480, S.481 Chain C: K.465, M.466, R.467, G.468, S.469, W.470, H.471 Ligands: MG.8 19 PLIP interactions: 14 interactions with chain B, 5 interactions with chain C Hydrogen bonds: B:G.299, B:G.299, B:T.300, B:G.301, B:K.302, B:T.303, B:T.303, B:L.304, B:E.326, B:E.327, B:S.338, B:R.459, C:M.466, C:G.468, C:H.471 Salt bridges: B:K.302, B:K.302, C:K.465, C:R.467 ATP.9: 22 residues within 4Å: Chain C: S.56, G.57, T.58, G.59, K.60, T.61, L.62, E.86, S.97, F.98, R.226, I.247 Chain D: F.207, L.231, K.232, L.233, R.234, G.235, T.236, S.237, H.238 Ligands: MG.11 20 PLIP interactions: 7 interactions with chain D, 13 interactions with chain C Hydrogen bonds: D:E.206, D:L.233, D:G.235, D:H.238, C:G.57, C:G.57, C:T.58, C:G.59, C:K.60, C:T.61, C:T.61, C:L.62, C:S.97, C:S.97, C:R.226 Salt bridges: D:K.232, D:K.232, D:R.234, C:K.60, C:K.60 ATP.10: 23 residues within 4Å: Chain C: A.297, T.298, G.299, T.300, G.301, K.302, T.303, L.304, E.326, E.327, S.338, W.339, R.459, I.480, S.481 Chain D: K.465, M.466, R.467, G.468, S.469, W.470, H.471 Ligands: MG.12 19 PLIP interactions: 14 interactions with chain C, 5 interactions with chain D Hydrogen bonds: C:G.299, C:G.299, C:T.300, C:G.301, C:K.302, C:T.303, C:T.303, C:L.304, C:E.326, C:E.327, C:S.338, C:R.459, D:M.466, D:G.468, D:H.471 Salt bridges: C:K.302, C:K.302, D:K.465, D:R.467 ATP.13: 22 residues within 4Å: Chain D: S.56, G.57, T.58, G.59, K.60, T.61, L.62, E.86, S.97, F.98, R.226, I.247 Chain E: F.207, L.231, K.232, L.233, R.234, G.235, T.236, S.237, H.238 Ligands: MG.15 20 PLIP interactions: 7 interactions with chain E, 13 interactions with chain D Hydrogen bonds: E:E.206, E:L.233, E:G.235, E:H.238, D:G.57, D:G.57, D:T.58, D:G.59, D:K.60, D:T.61, D:T.61, D:L.62, D:S.97, D:S.97, D:R.226 Salt bridges: E:K.232, E:K.232, E:R.234, D:K.60, D:K.60 ATP.14: 23 residues within 4Å: Chain D: A.297, T.298, G.299, T.300, G.301, K.302, T.303, L.304, E.326, E.327, S.338, W.339, R.459, I.480, S.481 Chain E: K.465, M.466, R.467, G.468, S.469, W.470, H.471 Ligands: MG.16 20 PLIP interactions: 5 interactions with chain E, 15 interactions with chain D Hydrogen bonds: E:M.466, E:G.468, E:H.471, D:G.299, D:G.299, D:T.300, D:G.301, D:K.302, D:T.303, D:T.303, D:T.303, D:L.304, D:E.326, D:E.327, D:S.338, D:R.459 Salt bridges: E:K.465, E:R.467, D:K.302, D:K.302 ATP.17: 22 residues within 4Å: Chain E: S.56, G.57, T.58, G.59, K.60, T.61, L.62, E.86, S.97, F.98, R.226, I.247 Chain F: F.207, L.231, K.232, L.233, R.234, G.235, T.236, S.237, H.238 Ligands: MG.19 19 PLIP interactions: 6 interactions with chain F, 13 interactions with chain E Hydrogen bonds: F:E.206, F:L.233, F:G.235, F:H.238, E:G.57, E:G.57, E:T.58, E:G.59, E:K.60, E:T.61, E:T.61, E:L.62, E:S.97, E:S.97, E:R.226 Salt bridges: F:K.232, F:R.234, E:K.60, E:K.60 ATP.18: 23 residues within 4Å: Chain E: A.297, T.298, G.299, T.300, G.301, K.302, T.303, L.304, E.326, E.327, S.338, W.339, R.459, I.480, S.481 Chain F: K.465, M.466, R.467, G.468, S.469, W.470, H.471 Ligands: MG.20 19 PLIP interactions: 5 interactions with chain F, 14 interactions with chain E Hydrogen bonds: F:M.466, F:G.468, F:H.471, E:G.299, E:G.299, E:T.300, E:G.301, E:K.302, E:T.303, E:T.303, E:L.304, E:E.326, E:E.327, E:S.338, E:R.459 Salt bridges: F:K.465, F:R.467, E:K.302, E:K.302 ATP.21: 22 residues within 4Å: Chain A: F.207, L.231, K.232, L.233, R.234, G.235, T.236, S.237, H.238 Chain F: S.56, G.57, T.58, G.59, K.60, T.61, L.62, E.86, S.97, F.98, R.226, I.247 Ligands: MG.23 19 PLIP interactions: 13 interactions with chain F, 6 interactions with chain A Hydrogen bonds: F:G.57, F:G.57, F:T.58, F:G.59, F:K.60, F:T.61, F:T.61, F:L.62, F:S.97, F:S.97, F:R.226, A:E.206, A:L.233, A:G.235, A:H.238 Salt bridges: F:K.60, F:K.60, A:K.232, A:R.234 ATP.22: 23 residues within 4Å: Chain A: K.465, M.466, R.467, G.468, S.469, W.470, H.471 Chain F: A.297, T.298, G.299, T.300, G.301, K.302, T.303, L.304, E.326, E.327, S.338, W.339, R.459, I.480, S.481 Ligands: MG.24 19 PLIP interactions: 5 interactions with chain A, 14 interactions with chain F Hydrogen bonds: A:M.466, A:G.468, A:H.471, F:G.299, F:G.299, F:T.300, F:G.301, F:K.302, F:T.303, F:T.303, F:L.304, F:E.326, F:E.327, F:S.338, F:R.459 Salt bridges: A:K.465, A:R.467, F:K.302, F:K.302

12 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: T.61, E.86, D.153 Ligands: ATP.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.61 MG.4: 5 residues within 4Å: Chain A: T.303, E.326, E.327, D.386 Ligands: ATP.2 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:T.303, A:E.326 MG.7: 4 residues within 4Å: Chain B: T.61, E.86, D.153 Ligands: ATP.5 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.61 MG.8: 5 residues within 4Å: Chain B: T.303, E.326, E.327, D.386 Ligands: ATP.6 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:T.303, B:E.326 MG.11: 4 residues within 4Å: Chain C: T.61, E.86, D.153 Ligands: ATP.9 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.61 MG.12: 5 residues within 4Å: Chain C: T.303, E.326, E.327, D.386 Ligands: ATP.10 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:T.303, C:E.326 MG.15: 4 residues within 4Å: Chain D: T.61, E.86, D.153 Ligands: ATP.13 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.61 MG.16: 5 residues within 4Å: Chain D: T.303, E.326, E.327, D.386 Ligands: ATP.14 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:T.303, D:E.326 MG.19: 4 residues within 4Å: Chain E: T.61, E.86, D.153 Ligands: ATP.17 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:T.61 MG.20: 5 residues within 4Å: Chain E: T.303, E.326, E.327, D.386 Ligands: ATP.18 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:T.303, E:E.326 MG.23: 4 residues within 4Å: Chain F: T.61, E.86, D.153 Ligands: ATP.21 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:T.61 MG.24: 5 residues within 4Å: Chain F: T.303, E.326, E.327, D.386 Ligands: ATP.22 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:T.303, F:E.326

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dzimianski, J.V. et al., Extended conformation of dusk state KaiC. To Be Published

Release Date

2025-05-14

Peptides

Circadian clock oscillator protein KaiC: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Circadian clock oscillator protein KaiC

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