SMTL ID : 4dl9.1

Crystal structure of S-nitrosoglutathione reductase from tomato (Solanum lycopersicum) in complex with NAD+

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-dimer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: C.64, H.86, E.87, C.194, R.389 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.64, A:H.86, A:E.87, A:C.194 ZN.2: 5 residues within 4Å: Chain A: C.116, R.117, 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.6: 5 residues within 4Å: Chain B: C.64, H.86, E.87, C.194, R.389 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.64, B:H.86, B:E.87, B:C.194 ZN.7: 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: Y.112, C.194, T.198, G.219, L.220, G.221, T.222, V.223, I.242, D.243, I.244, K.248, C.288, I.289, G.290, V.294, V.312, G.313, V.314, T.337, A.338, F.339, R.389 22 PLIP interactions: 22 interactions with chain A Hydrophobic interactions: A:T.198 Hydrogen bonds: A:L.220, A:T.222, A:V.223, A:I.244, A:K.248, A:I.289, A:V.312, A:V.314, A:F.339 Water bridges: A:H.65, A:H.65, A:G.221, A:T.222, A:G.224, A:N.291, A:N.291, A:N.291, A:R.389, A:R.389, A:R.389 Salt bridges: A:R.389 NAD.8: 23 residues within 4Å: Chain B: Y.112, C.194, T.198, G.219, L.220, G.221, T.222, V.223, I.242, D.243, I.244, K.248, C.288, I.289, G.290, V.294, V.312, G.313, V.314, T.337, A.338, F.339, R.389 22 PLIP interactions: 22 interactions with chain B Hydrophobic interactions: B:T.198 Hydrogen bonds: B:H.65, B:Y.112, B:T.198, B:L.220, B:L.220, B:G.221, B:T.222, B:V.223, B:I.244, B:I.289, B:V.312, B:V.314, B:F.339, B:R.389 Water bridges: B:G.221, B:G.221, B:K.248, B:N.291, B:N.291, B:N.291, B:R.389

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 4 residues within 4Å: Chain A: W.204, A.233, A.234, K.354 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.354, A:K.354 Water bridges: A:V.209, A:A.234 GOL.9: 4 residues within 4Å: Chain B: W.204, A.233, A.234, K.354 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:A.233, B:K.354, B:K.354 Water bridges: B:V.209, B:A.233

2 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.5: 5 residues within 4Å: Chain A: R.324, F.326 Chain B: E.77, S.317, G.318 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:G.318 Water bridges: B:Q.319, A:F.326 Salt bridges: A:R.324 MES.10: 5 residues within 4Å: Chain A: E.77, S.317, G.318 Chain B: R.324, F.326 6 PLIP interactions: 2 interactions with chain B, 4 interactions with chain A Water bridges: B:F.326, A:A.315, A:A.316, A:S.317 Salt bridges: B:R.324 Hydrogen bonds: A:G.318

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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