SMTL ID : 1wwj.1

crystal structure of KaiB from Synechocystis sp.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-tetramer

Ligands

8 x MLT: D-MALATE(Non-covalent)

MLT.1: 3 residues within 4Å: Chain A: N.50, P.51, Q.52 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Q.52 Hydrogen bonds: A:N.50, A:Q.52, A:Q.52, A:Q.52 MLT.3: 3 residues within 4Å: Chain B: N.17, T.18, P.19 No protein-ligand interaction detected (PLIP) MLT.4: 9 residues within 4Å: Chain B: V.14, G.16, N.17, S.21, L.25, V.44, D.46, K.49, V.86 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:N.17, B:L.25 Hydrogen bonds: B:G.16, B:G.16, B:N.17, B:S.21, B:D.46 Salt bridges: B:K.49 MLT.5: 2 residues within 4Å: Chain B: E.35 Ligands: BET.9 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.35 MLT.6: 10 residues within 4Å: Chain B: E.56, K.58, L.93, Y.94, D.95 Chain C: K.67, I.68, L.69, P.70, P.71 9 PLIP interactions: 8 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:L.93 Hydrogen bonds: B:K.58, B:Y.94, B:D.95, C:L.69 Water bridges: B:K.11, B:K.11, B:E.56, B:D.57 MLT.11: 8 residues within 4Å: Chain C: K.11, Y.13, K.43, I.45, N.50, Q.52, L.53, D.57 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:I.45 Hydrogen bonds: C:Y.13, C:D.57, C:D.57 Water bridges: C:K.43 Salt bridges: C:K.11, C:K.43 MLT.12: 6 residues within 4Å: Chain C: K.43, V.44, I.45, D.46, K.49, N.50 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:D.46, C:D.46, C:K.49 Water bridges: C:K.43, C:V.44 Salt bridges: C:K.43, C:K.43, C:K.49 MLT.14: 5 residues within 4Å: Chain C: L.48, K.49, P.51, Q.52 Chain D: K.85 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:K.85 Hydrogen bonds: D:K.85 Salt bridges: D:K.85 Water bridges: C:Q.52, C:Q.52

5 x BET: TRIMETHYL GLYCINE(Non-covalent)

BET.2: 3 residues within 4Å: Chain A: Q.34 Chain D: Y.8 Ligands: BET.16 2 PLIP interactions: 2 interactions with chain A Water bridges: A:E.35, A:E.35 BET.9: 3 residues within 4Å: Chain B: Q.34, E.35 Ligands: MLT.5 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:E.35 BET.10: 7 residues within 4Å: Chain B: Y.40, K.67, I.68, L.69, P.70, R.74 Ligands: IMD.7 No protein-ligand interaction detected (PLIP) BET.13: 4 residues within 4Å: Chain C: T.18, P.19, N.20, E.84 1 PLIP interactions: 1 interactions with chain C Salt bridges: C:E.84 BET.16: 6 residues within 4Å: Chain A: E.35, Q.37 Chain D: Y.8, Y.40, I.68 Ligands: BET.2 No protein-ligand interaction detected (PLIP)

3 x IMD: IMIDAZOLE(Non-covalent)

IMD.7: 5 residues within 4Å: Chain B: Y.8, Y.40 Chain C: E.35, Q.37 Ligands: BET.10 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:Y.40, B:I.68, C:Q.37 IMD.8: 4 residues within 4Å: Chain B: K.75, G.78, D.79, R.83 No protein-ligand interaction detected (PLIP) IMD.15: 2 residues within 4Å: Chain D: V.44, D.46 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hitomi, K. et al., Tetrameric architecture of the circadian clock protein KaiB. A novel interface for intermolecular interactions and its impact on the circadian rhythm. J.Biol.Chem. (2005)

Release Date

2005-02-15

Peptides

Circadian clock protein kaiB: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Circadian clock protein kaiB