SMTL ID : 8co4.1 (1 other biounit)

Crystal structure of apo S-nitrosoglutathione reductase from Arabidopsis thalina

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: C.99, R.100, C.102, C.105, C.113 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.99, A:C.102, A:C.105, A:C.113 ZN.2: 4 residues within 4Å: Chain A: C.47, H.69, E.70, C.177 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:C.47, A:H.69, A:C.177, H2O.1, H2O.7 ZN.12: 6 residues within 4Å: Chain B: C.99, R.100, C.102, C.105, C.113, G.114 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.99, B:C.102, B:C.105, B:C.113 ZN.13: 4 residues within 4Å: Chain B: C.47, T.49, H.69, C.177 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:C.47, B:H.69, B:C.177, H2O.12, H2O.13

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 4 residues within 4Å: Chain A: E.212, T.216, E.342, K.344 2 PLIP interactions: 2 interactions with chain A Water bridges: A:E.212, A:E.212

6 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.4: 3 residues within 4Å: Chain A: I.124, P.139, Y.141 2 PLIP interactions: 2 interactions with chain A Water bridges: A:S.131, A:P.139 PEG.5: 6 residues within 4Å: Chain A: E.193, P.194, S.196, D.266, Y.267 Chain B: K.109 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:P.194, A:Y.267 Water bridges: A:Y.267 PEG.6: 5 residues within 4Å: Chain A: K.287 Chain B: F.104, C.113, G.114, R.117 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:K.287, B:R.117 PEG.7: 4 residues within 4Å: Chain A: Y.338, M.339, K.341 Ligands: PGE.8 2 PLIP interactions: 2 interactions with chain A Water bridges: A:Y.338, A:Y.338 PEG.14: 5 residues within 4Å: Chain A: F.104, L.112, G.114 Chain B: K.287, T.313 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:K.287 Water bridges: A:C.113 PEG.15: 2 residues within 4Å: Chain B: Y.16, V.23 No protein-ligand interaction detected (PLIP)

5 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.8: 2 residues within 4Å: Chain A: K.341 Ligands: PEG.7 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.341 Water bridges: A:K.341 PGE.9: 4 residues within 4Å: Chain A: L.62, V.122, I.124, Y.141 No protein-ligand interaction detected (PLIP) PGE.10: 7 residues within 4Å: Chain A: K.109 Chain B: E.193, P.194, S.196, D.266, Y.267, W.289 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:K.109 Water bridges: B:Y.267 PGE.16: 5 residues within 4Å: Chain B: K.130, S.131, K.138, P.139, Y.141 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.131 PGE.17: 3 residues within 4Å: Chain B: Y.338, M.339, K.341 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.341

1 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.11: 2 residues within 4Å: Chain A: K.40, Y.152 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.40

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Meloni, M. et al., Structural and biochemical characterization of Arabidopsis alcohol dehydrogenases reveals distinct functional properties but similar redox sensitivity. Plant J. (2024)

Release Date

2024-02-21

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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