SMTL ID : 4dlb.1

Structure of S-nitrosoglutathione reductase from tomato (Solanum lycopersicum) crystallized in presence of NADH and glutathione

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.64, H.86, E.87, C.194 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:C.64, A:H.86, A:C.194, H2O.8 ZN.2: 4 residues within 4Å: Chain A: C.116, C.119, C.122, C.130 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.116, A:C.119, A:C.122, A:C.130 ZN.7: 5 residues within 4Å: Chain B: C.64, H.86, E.87, C.194, R.389 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:C.64, B:H.86, B:E.87, B:C.194, H2O.14 ZN.8: 4 residues within 4Å: Chain B: C.116, C.119, C.122, C.130 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.116, B:C.119, B:C.122, B:C.130

2 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)

NAD.3: 23 residues within 4Å: Chain A: H.65, T.66, Y.112, C.194, T.198, G.219, G.221, T.222, V.223, I.242, D.243, I.244, K.248, C.288, I.289, V.294, V.312, G.313, V.314, T.337, A.338, F.339, R.389 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:T.198 Hydrogen bonds: A:H.65, A:L.220, A:T.222, A:V.223, A:I.244, A:K.248, A:I.289, A:N.291, A:V.312, A:V.314, A:F.339 Water bridges: A:G.221, A:G.221, A:R.389, A:R.389 Salt bridges: A:K.248, A:R.389 NAD.9: 23 residues within 4Å: Chain B: H.65, T.66, Y.112, C.194, T.198, G.219, L.220, G.221, T.222, V.223, D.243, I.244, K.248, C.288, I.289, V.294, V.312, G.313, V.314, T.337, A.338, F.339, R.389 19 PLIP interactions: 19 interactions with chain B Hydrophobic interactions: B:T.198 Hydrogen bonds: B:T.66, B:Y.112, B:T.198, B:L.220, B:G.221, B:T.222, B:V.223, B:I.244, B:K.248, B:I.289, B:V.312, B:V.314, B:F.339 Water bridges: B:T.222, B:G.224, B:N.291, B:R.389 Salt bridges: B:R.389

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 4 residues within 4Å: Chain A: K.188, D.363, I.366, N.369 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.363, A:N.369 GOL.5: 3 residues within 4Å: Chain A: W.204, A.234, K.354 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:W.204, A:K.354 Water bridges: A:V.209 GOL.6: 4 residues within 4Å: Chain A: E.229, K.358, E.359, K.361 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.229 GOL.10: 8 residues within 4Å: Chain B: E.77, L.79, T.137, G.138, G.140, H.159, F.160, M.161 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:M.161 Water bridges: B:T.70, B:D.75, B:G.140, B:H.159 GOL.11: 4 residues within 4Å: Chain B: K.188, D.363, I.366, N.369 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.188, B:I.366, B:N.369

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kubienova, L. et al., Structural and functional characterization of a plant S-nitrosoglutathione reductase from Solanum lycopersicum. Biochimie (2013)

Release Date

2012-12-26

Peptides

Alcohol dehydrogenase class III: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Alcohol dehydrogenase class III

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