SMTL ID : 4kcf.4 (3 other biounits)

X-ray Structure of a KijD3 in Complex with FMN and dTDP-3-amino-2,3,6-trideoxy-4-keto-3-methyl-D-glucose

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

2 x AKM: [(2R,4S,6R)-4-azanyl-4,6-dimethyl-5,5-bis(oxidanyl)oxan-2-yl] [[(2R,3S,5R)-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] hydrogen phosphate(Non-covalent)

AKM.1: 21 residues within 4Å: Chain A: H.118, M.119, S.122, R.123, T.126, Y.129, E.130, S.158, I.160, V.197, R.257, A.266, A.269, G.270, Q.271, V.273, S.274, S.275, R.347, M.427 Ligands: FMN.2 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:I.160 Hydrogen bonds: A:E.130, A:S.158, A:S.158, A:R.257, A:R.257, A:Q.271, A:S.274, A:S.275, A:R.347, A:R.347 Water bridges: A:G.270, A:Q.271, A:S.274, A:Q.402 Salt bridges: A:R.123, A:R.123 pi-Stacking: A:Y.129 AKM.3: 21 residues within 4Å: Chain B: H.118, M.119, S.122, R.123, T.126, Y.129, E.130, S.158, I.160, V.197, R.257, A.266, A.269, G.270, Q.271, V.273, S.274, S.275, R.347, M.427 Ligands: FMN.4 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:I.160 Hydrogen bonds: B:E.130, B:S.158, B:S.158, B:R.257, B:R.257, B:Q.271, B:S.274, B:S.275, B:R.347, B:R.347 Water bridges: B:G.270, B:Q.271, B:S.274, B:Q.402 Salt bridges: B:R.123, B:R.123 pi-Stacking: B:Y.129

2 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.2: 16 residues within 4Å: Chain A: L.115, M.119, S.158, I.160, K.161, L.186, V.187, S.188, M.234, T.239, F.400, M.401, Q.402, W.430 Chain B: Y.382 Ligands: AKM.1 9 PLIP interactions: 8 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:M.234, A:T.239, B:Y.382 Hydrogen bonds: A:S.158, A:I.160, A:S.188, A:Q.402 Water bridges: A:K.161, A:Q.402 FMN.4: 16 residues within 4Å: Chain A: Y.382 Chain B: L.115, M.119, S.158, I.160, K.161, L.186, V.187, S.188, M.234, T.239, F.400, M.401, Q.402, W.430 Ligands: AKM.3 9 PLIP interactions: 1 interactions with chain A, 8 interactions with chain B Hydrophobic interactions: A:Y.382, B:M.234, B:T.239 Hydrogen bonds: B:S.158, B:I.160, B:S.188, B:Q.402 Water bridges: B:K.161, B:Q.402

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Thoden, J.B. et al., Active site architecture of a sugar N-oxygenase. Biochemistry (2013)

Release Date

2013-05-22

Peptides

FAD-dependent oxidoreductase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

FAD-dependent oxidoreductase

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