SMTL ID : 2zts.1

Crystal structure of KaiC-like protein PH0186 from hyperthermophilic archaea Pyrococcus horikoshii OT3

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.07 Å

Oligo State

homo-hexamer

Ligands

6 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.1: 20 residues within 4Å: Chain A: G.38, T.39, G.40, T.41, G.42, K.43, T.44, T.45, S.80, F.81, R.216, I.237, G.238 Chain F: K.222, M.223, E.225, T.226, R.227, H.228 Ligands: MG.2 23 PLIP interactions: 8 interactions with chain F, 15 interactions with chain A Hydrogen bonds: F:E.225, F:T.226, F:H.228, A:G.40, A:T.41, A:T.41, A:G.42, A:K.43, A:T.44, A:T.45, A:T.45, A:S.80, A:S.80, A:R.216 Water bridges: F:K.222, F:K.222, F:K.222, A:T.44, A:E.180, A:R.216 Salt bridges: F:K.222, F:K.222, A:K.43 ADP.3: 19 residues within 4Å: Chain A: K.222, M.223, E.225, T.226, R.227, H.228 Chain B: G.38, T.39, G.40, T.41, G.42, K.43, T.44, T.45, S.80, F.81, R.216, I.237 Ligands: MG.4 22 PLIP interactions: 15 interactions with chain B, 7 interactions with chain A Hydrogen bonds: B:G.40, B:T.41, B:T.41, B:G.42, B:K.43, B:T.44, B:T.45, B:T.45, B:S.80, B:S.80, B:R.216, A:E.225, A:T.226, A:H.228 Water bridges: B:T.44, B:E.180, B:R.216, A:K.222, A:K.222 Salt bridges: B:K.43, A:K.222, A:K.222 ADP.5: 20 residues within 4Å: Chain B: K.222, M.223, E.225, T.226, R.227, H.228 Chain C: G.38, T.39, G.40, T.41, G.42, K.43, T.44, T.45, S.80, F.81, R.216, I.237, G.238 Ligands: MG.6 24 PLIP interactions: 14 interactions with chain C, 10 interactions with chain B Hydrogen bonds: C:G.40, C:T.41, C:G.42, C:K.43, C:T.44, C:T.45, C:T.45, C:S.80, C:S.80, C:R.216, B:E.225, B:T.226, B:H.228 Water bridges: C:T.44, C:E.180, C:R.216, B:K.222, B:K.222, B:K.222, B:R.227, B:H.228 Salt bridges: C:K.43, B:K.222, B:K.222 ADP.7: 20 residues within 4Å: Chain C: K.222, M.223, E.225, T.226, R.227, H.228 Chain D: G.38, T.39, G.40, T.41, G.42, K.43, T.44, T.45, S.80, F.81, R.216, I.237, G.238 Ligands: MG.8 22 PLIP interactions: 8 interactions with chain C, 14 interactions with chain D Hydrogen bonds: C:E.225, C:T.226, C:H.228, D:G.40, D:T.41, D:G.42, D:K.43, D:T.44, D:T.45, D:T.45, D:S.80, D:S.80, D:R.216 Water bridges: C:K.222, C:K.222, C:K.222, D:T.44, D:T.44, D:R.216 Salt bridges: C:K.222, C:K.222, D:K.43 ADP.9: 19 residues within 4Å: Chain D: K.222, M.223, E.225, T.226, R.227, H.228 Chain E: G.38, T.39, G.40, T.41, G.42, K.43, T.44, T.45, S.80, F.81, R.216, I.237 Ligands: MG.10 22 PLIP interactions: 14 interactions with chain E, 8 interactions with chain D Hydrogen bonds: E:G.40, E:T.41, E:G.42, E:K.43, E:T.44, E:T.44, E:T.45, E:T.45, E:S.80, E:S.80, E:R.216, D:E.225, D:T.226, D:H.228 Water bridges: E:E.180, E:R.216, D:K.222, D:K.222, D:K.222 Salt bridges: E:K.43, D:K.222, D:K.222 ADP.11: 20 residues within 4Å: Chain E: K.222, M.223, E.225, T.226, R.227, H.228 Chain F: G.38, T.39, G.40, T.41, G.42, K.43, T.44, T.45, S.80, F.81, R.216, I.237, G.238 Ligands: MG.12 25 PLIP interactions: 15 interactions with chain F, 10 interactions with chain E Hydrogen bonds: F:G.40, F:T.41, F:T.41, F:G.42, F:K.43, F:T.44, F:T.44, F:T.45, F:T.45, F:S.80, F:S.80, F:R.216, E:E.225, E:T.226, E:H.228 Water bridges: F:E.180, F:R.216, E:K.222, E:K.222, E:K.222, E:R.227, E:H.228 Salt bridges: F:K.43, E:K.222, E:K.222

6 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: T.44, D.142 Ligands: ADP.1 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:T.44, H2O.1, H2O.1, H2O.1, H2O.1 MG.4: 3 residues within 4Å: Chain A: K.222 Chain B: T.44 Ligands: ADP.3 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:T.44, H2O.2, H2O.3, H2O.3, H2O.3 MG.6: 2 residues within 4Å: Chain C: T.44 Ligands: ADP.5 5 PLIP interactions: 1 interactions with chain C, 4 Ligand-Water interactions Metal complexes: C:T.44, H2O.4, H2O.4, H2O.4, H2O.4 MG.8: 3 residues within 4Å: Chain D: T.44, D.142 Ligands: ADP.7 5 PLIP interactions: 1 interactions with chain D, 4 Ligand-Water interactions Metal complexes: D:T.44, H2O.4, H2O.5, H2O.5, H2O.5 MG.10: 3 residues within 4Å: Chain D: K.222 Chain E: T.44 Ligands: ADP.9 5 PLIP interactions: 1 interactions with chain E, 4 Ligand-Water interactions Metal complexes: E:T.44, H2O.5, H2O.6, H2O.6, H2O.6 MG.12: 2 residues within 4Å: Chain F: T.44 Ligands: ADP.11 5 PLIP interactions: 1 interactions with chain F, 4 Ligand-Water interactions Metal complexes: F:T.44, H2O.7, H2O.7, H2O.7, H2O.7

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kang, H.-J. et al., Crystal structure of KaiC-like protein PH0186 from hyperthermophilic archaea Pyrococcus horikoshii OT3. Proteins (2009)

Release Date

2009-03-24

Peptides

Putative uncharacterized protein PH0186: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
A

E
B

F
C

Putative uncharacterized protein PH0186