SMTL ID : 4v37.1 (1 other biounit)

Crystal structure of betaine aldehyde dehydrogenase from spinach showing a thiohemiacetal with 3-aminopropionaldehyde

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

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

NAD.1: 29 residues within 4Å: Chain A: I.155, S.156, P.157, W.158, N.159, M.164, K.182, P.183, S.184, E.185, G.215, G.219, A.220, V.223, F.233, T.234, G.235, S.236, T.239, K.242, V.243, E.257, L.258, G.259, A.291, E.390, F.392, W.456 Ligands: FMT.3 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:P.157, A:T.234, A:A.291 Hydrogen bonds: A:S.156, A:W.158, A:K.182, A:E.185, A:S.236, A:T.239, A:L.258, A:E.390 Water bridges: A:G.215, A:G.215, A:S.237, A:K.242, A:E.390 NAD.6: 28 residues within 4Å: Chain B: I.155, S.156, P.157, W.158, N.159, M.164, K.182, P.183, S.184, E.185, G.215, G.219, A.220, F.233, T.234, G.235, S.236, T.239, V.243, E.257, L.258, G.259, A.291, E.390, F.392, L.418, W.456 Ligands: FMT.8 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:P.157, B:T.234, B:A.291 Hydrogen bonds: B:S.156, B:W.158, B:K.182, B:E.185, B:S.236, B:T.239, B:T.239, B:L.258, B:E.390 Water bridges: B:S.184, B:S.237

2 x 0D8: 3-aminopropan-1-ol(Covalent)

0D8.2: 6 residues within 4Å: Chain A: W.167, S.292, C.450, F.451, W.456 Ligands: FMT.3 6 PLIP interactions: 1 interactions with chain B, 5 interactions with chain A Hydrogen bonds: B:Q.481, A:S.292, A:F.451 Hydrophobic interactions: A:W.456 Water bridges: A:S.292, A:Q.448 0D8.7: 5 residues within 4Å: Chain B: W.167, S.292, C.450, W.456 Ligands: FMT.8 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:W.456 Hydrogen bonds: B:S.292, B:F.451, A:Q.481 Water bridges: B:S.292, B:Q.448

2 x FMT: FORMIC ACID(Non-functional Binders)

FMT.3: 7 residues within 4Å: Chain A: N.159, Y.160, I.290, A.291, S.292 Ligands: NAD.1, 0D8.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.159, A:A.291, A:S.292 FMT.8: 7 residues within 4Å: Chain B: N.159, Y.160, I.290, A.291, S.292 Ligands: NAD.6, 0D8.7 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.159, B:A.291, B:S.292

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

PG4.4: 8 residues within 4Å: Chain A: R.146, E.470, W.471, Q.474 Chain B: R.146, E.470, W.471, Q.474 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.474

2 x K: POTASSIUM ION(Non-covalent)

K.5: 3 residues within 4Å: Chain A: I.28, D.96, L.186 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:I.28, A:D.96, A:D.96, A:L.186, H2O.2 K.10: 3 residues within 4Å: Chain B: I.28, D.96, L.186 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:I.28, B:D.96, B:D.96, B:L.186, H2O.15

1 x AE3: 2-(2-ETHOXYETHOXY)ETHANOL(Non-covalent)

AE3.9: 8 residues within 4Å: Chain A: W.491 Chain B: Y.160, L.163, W.285, Q.448, P.449, C.450, F.451 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:C.450

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zarate-Romero, A. et al., Identification of a Stable Thiohemiacetal Involving a Conserved Cysteine in the Substrate Inactivation of S. Oleracea Betaine Aldehyde Dehydrogenase. To be Published

Release Date

2016-01-20

Peptides

BETAINE ALDEHYDE DEHYDROGENASE, CHLOROPLASTIC: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

BETAINE ALDEHYDE DEHYDROGENASE, CHLOROPLASTIC

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