SMTL ID : 4a0g.1 (1 other biounit)

Structure of bifunctional DAPA aminotransferase-DTB synthetase from Arabidopsis thaliana in its apo form.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-dimer

Ligands

2 x PLP: PYRIDOXAL-5'-PHOSPHATE(Covalent)

PLP.1: 13 residues within 4Å: Chain A: N.450, G.451, S.452, Y.493, H.494, G.495, E.601, D.635, V.637, F.638, K.664 Chain B: H.699, S.700 16 PLIP interactions: 11 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:E.601, A:V.637, A:F.638, A:K.664 Hydrogen bonds: A:G.451, A:S.452, B:S.700, B:S.700 Water bridges: A:Y.493, A:Y.493, A:Y.493, B:S.700, B:Y.701 Salt bridges: A:K.664, B:H.699 pi-Stacking: A:Y.493 PLP.5: 14 residues within 4Å: Chain A: H.699, S.700 Chain B: W.390, N.450, G.451, S.452, Y.493, H.494, G.495, E.601, D.635, V.637, F.638, K.664 17 PLIP interactions: 13 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:E.601, B:V.637, B:F.638, B:K.664 Hydrogen bonds: B:G.451, B:S.452, A:S.700, A:S.700 Water bridges: B:N.450, B:N.450, B:Y.493, B:Y.493, B:Y.493, A:S.700 Salt bridges: B:K.664, A:H.699 pi-Stacking: B:Y.493

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

SO4.2: 6 residues within 4Å: Chain A: T.44, K.48, K.75, A.210, G.211 Ligands: SO4.4 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.44, A:G.211 Salt bridges: A:K.48, A:K.75 SO4.3: 8 residues within 4Å: Chain A: L.242, G.243, G.244, I.245, S.246 Chain B: S.163, S.215, P.216 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:G.243, A:G.244, A:I.245, A:S.246, B:S.163 SO4.4: 7 residues within 4Å: Chain A: S.45, L.46, G.47, K.48, T.49, L.50 Ligands: SO4.2 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:S.45, A:L.46, A:G.47, A:K.48, A:T.49, A:T.49, A:L.50 SO4.6: 7 residues within 4Å: Chain A: S.215, P.216 Chain B: L.242, G.243, G.244, I.245, S.246 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:G.243, B:G.243, B:G.244, B:I.245, B:S.246 Water bridges: B:N.274 SO4.7: 8 residues within 4Å: Chain B: K.48, K.75, D.86, E.208, T.209, A.210, G.211 Ligands: MG.8 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.211 Salt bridges: B:K.48, B:K.75

1 x MG: MAGNESIUM ION(Non-covalent)

MG.8: 5 residues within 4Å: Chain B: K.48, T.49, D.86, E.208 Ligands: SO4.7 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:T.49, B:E.208, H2O.8

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cobessi, D. et al., Biochemical and Structural Characterization of the Arabidopsis Bifunctional Enzyme Dethiobiotin Synthetase-Diaminopelargonic Acid Aminotransferase: Evidence for Substrate Channeling in Biotin Synthesis. Plant Cell (2012)

Release Date

2012-06-13

Peptides

ADENOSYLMETHIONINE-8-AMINO-7-OXONONANOATE AMINOTRANSFERASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

ADENOSYLMETHIONINE-8-AMINO-7-OXONONANOATE AMINOTRANSFERASE

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