SMTL ID : 4i9b.1

Structure of aminoaldehyde dehydrogenase 1 from Solanum lycopersium (SlAMADH1) with a thiohemiacetal intermediate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

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

NAD.1: 17 residues within 4Å: Chain A: I.171, T.172, W.174, K.198, P.199, S.200, E.201, G.231, P.232, G.235, G.236, F.249, T.250, G.251, S.252, T.255, I.259 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:T.172, A:W.174, A:K.198, A:E.201, A:S.252, A:T.255 Water bridges: A:K.258 NAD.6: 18 residues within 4Å: Chain B: I.171, T.172, W.174, K.198, P.199, S.200, E.201, G.231, P.232, G.235, G.236, F.249, T.250, G.251, S.252, T.255, K.258, I.259 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:T.172, B:W.174, B:K.198, B:E.201, B:S.252, B:T.255, B:T.255 Water bridges: B:K.258, B:K.258

2 x NA: SODIUM ION(Non-functional Binders)

NA.2: 3 residues within 4Å: Chain A: I.44, D.112, L.202 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:I.44, A:D.112, A:D.112 NA.7: 3 residues within 4Å: Chain B: I.44, D.112, L.202 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.112

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

PEG.3: 8 residues within 4Å: Chain A: A.321, M.325, T.395, D.396, V.397, V.415, K.416, T.417 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.396, A:V.397, A:V.397 Water bridges: A:T.417 PEG.8: 6 residues within 4Å: Chain A: Y.156, L.508 Chain B: F.298, P.466, T.467, F.468 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Water bridges: B:T.467 Hydrogen bonds: A:Y.156

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

EDO.4: 3 residues within 4Å: Chain A: P.466 Chain B: Y.156, L.508 2 PLIP interactions: 2 interactions with chain A Water bridges: A:T.467, A:T.467

2 x 1KA: (2-hydroxyethoxy)acetaldehyde(Non-covalent)

1KA.5: 7 residues within 4Å: Chain A: N.175, Y.176, W.183, V.307, C.308, S.309, W.473 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.175, A:C.308 1KA.9: 6 residues within 4Å: Chain B: Y.176, W.183, V.307, C.308, S.309, W.473 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:C.308, B:S.309

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kopecny, D. et al., Plant ALDH10 family: identifying critical residues for substrate specificity and trapping a thiohemiacetal intermediate. J.Biol.Chem. (2013)

Release Date

2013-02-20

Peptides

Putative betaine aldehyde dehyrogenase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Putative betaine aldehyde dehyrogenase