SMTL ID : 4g86.1

Crystal structure of the redox-active cofactor DBMIB bound to the full length circadian clock protein KaiA from Synechococcus elongatus

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.39 Å

Oligo State

homo-dimer

Ligands

4 x BNT: 2,5-DIBROMO-3-ISOPROPYL-6-METHYLBENZO-1,4-QUINONE(Non-covalent)

BNT.1: 6 residues within 4Å: Chain A: S.62, F.63, R.64, A.65, R.85, S.87 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:R.64, A:R.85 Hydrogen bonds: A:F.63, A:R.64 BNT.4: 5 residues within 4Å: Chain A: R.180, P.229, T.231 Chain B: E.274, R.277 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:P.229, A:T.231 Hydrogen bonds: B:R.277, B:R.277 BNT.5: 9 residues within 4Å: Chain A: E.112, Y.116 Chain B: L.182, E.186, K.189, L.190, A.193 Ligands: 1PE.2, 2PE.3 7 PLIP interactions: 2 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:E.112, A:Y.116, B:L.182, B:E.186, B:K.189, B:K.189, B:L.190 BNT.6: 10 residues within 4Å: Chain B: A.58, A.59, N.60, P.61, S.62, F.63, R.64, A.65, R.85, D.86 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:R.64 Hydrogen bonds: B:S.62, B:F.63, B:R.64

1 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.2: 7 residues within 4Å: Chain A: D.19, R.22, A.23, E.112, P.115 Ligands: 2PE.3, BNT.5 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:E.112 Water bridges: A:A.23, A:S.25, A:L.111, A:E.112, A:E.112

1 x 2PE: NONAETHYLENE GLYCOL(Non-covalent)

2PE.3: 5 residues within 4Å: Chain A: R.22 Chain B: Y.185, K.189 Ligands: 1PE.2, BNT.5 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:R.22, B:Y.185, B:K.189

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 7 residues within 4Å: Chain A: L.104, E.124 Chain B: D.217, N.221, M.275, R.278 Ligands: GOL.8 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:N.221, B:R.278 Water bridges: B:D.217, B:R.278, A:E.124 GOL.8: 7 residues within 4Å: Chain A: A.123, E.124, R.127 Chain B: M.275, R.278, S.279 Ligands: GOL.7 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:M.275, B:R.278 Water bridges: A:E.124

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pattanayek, R. et al., Crystal Structure of the Redox-Active Cofactor Dibromothymoquinone Bound to Circadian Clock Protein KaiA and Structural Basis for Dibromothymoquinone's Ability to Prevent Stimulation of KaiC Phosphorylation by KaiA. Biochemistry (2012)

Release Date

2012-10-24

Peptides

Circadian clock protein kaiA: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Circadian clock protein kaiA