SMTL ID : 4jji.1

Crystal structure of S-nitrosoglutathione reductase from Arabidopsis thalina, complex with NAD+

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: C.98, R.99, C.101, C.104, C.112 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.98, A:C.101, A:C.104, A:C.112 ZN.2: 5 residues within 4Å: Chain A: C.46, H.68, E.69, C.176, R.371 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:C.46, A:H.68, A:E.69, A:C.176, H2O.9 ZN.9: 5 residues within 4Å: Chain B: C.98, R.99, C.101, C.104, C.112 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.98, B:C.101, B:C.104, B:C.112 ZN.10: 5 residues within 4Å: Chain B: C.46, H.68, E.69, C.176, R.371 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.46, B:H.68, B:E.69, B:C.176

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

NAD.3: 23 residues within 4Å: Chain A: Y.94, C.176, T.180, G.201, L.202, G.203, T.204, V.205, I.224, D.225, I.226, K.230, C.270, I.271, G.272, V.276, V.294, G.295, V.296, T.319, A.320, F.321, R.371 25 PLIP interactions: 25 interactions with chain A Hydrophobic interactions: A:T.180 Hydrogen bonds: A:H.47, A:Y.94, A:T.180, A:L.202, A:G.203, A:T.204, A:V.205, A:I.226, A:K.230, A:I.271, A:N.273, A:V.294, A:V.296, A:F.321 Water bridges: A:H.47, A:G.206, A:K.230, A:V.296, A:R.371, A:R.371, A:R.371, A:R.371, A:R.371 Salt bridges: A:R.371 NAD.11: 20 residues within 4Å: Chain B: H.47, T.48, Y.51, G.201, G.203, T.204, V.205, I.224, D.225, I.226, K.230, C.270, I.271, V.276, V.294, G.295, V.296, A.297, A.298, R.371 21 PLIP interactions: 21 interactions with chain B Hydrophobic interactions: B:H.47 Hydrogen bonds: B:L.202, B:G.203, B:T.204, B:V.205, B:I.226, B:K.230, B:V.294, B:V.296 Water bridges: B:G.206, B:N.273, B:V.296, B:V.296, B:R.371, B:R.371, B:R.371, B:R.371 Salt bridges: B:H.47, B:H.47, B:K.230, B:R.371

9 x SO4: SULFATE ION(Non-functional Binders)

SO4.4: 3 residues within 4Å: Chain A: K.317 Chain B: V.315, K.317 7 PLIP interactions: 3 interactions with chain B, 4 interactions with chain A Water bridges: B:K.317, B:K.317, A:K.317, A:K.317, A:K.317 Salt bridges: B:K.317, A:K.317 SO4.5: 3 residues within 4Å: Chain A: S.275, R.278, S.304 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.275 Water bridges: A:S.304 Salt bridges: A:R.278 SO4.6: 3 residues within 4Å: Chain A: H.248, D.249, K.250 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.249, A:K.250 Salt bridges: A:H.248 SO4.7: 2 residues within 4Å: Chain A: C.101, K.102 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.102 SO4.8: 7 residues within 4Å: Chain A: R.306, P.307, F.308 Chain B: A.297, A.298, S.299, G.300 7 PLIP interactions: 2 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:F.308, B:A.298, B:S.299, B:G.300 Salt bridges: A:R.306 Water bridges: B:A.297, B:A.297 SO4.12: 3 residues within 4Å: Chain B: H.248, D.249, K.250 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.249, B:D.249, B:K.250 Salt bridges: B:H.248 SO4.13: 3 residues within 4Å: Chain B: S.275, R.278, S.304 4 PLIP interactions: 4 interactions with chain B Water bridges: B:S.275, B:A.279, B:S.304 Salt bridges: B:R.278 SO4.14: 2 residues within 4Å: Chain B: N.196, R.220 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.196, B:N.196 Water bridges: B:R.220 Salt bridges: B:R.220 SO4.15: 7 residues within 4Å: Chain A: V.311 Chain B: N.110, T.319, A.320, F.321, G.322, G.323 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:N.110, B:T.319, B:T.319, B:A.320, B:F.321, B:G.323

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Crotty, J. et al., Crystal structure and kinetic behavior of alcohol dehydrogenase III/S-nitrosoglutathione reductase from Arabidopsis thalina. To be Published

Release Date

2013-03-27

Peptides

Alcohol dehydrogenase class-3: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Alcohol dehydrogenase class-3

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