SMTL ID : 4pab.2 (1 other biounit)

Crystal structure of the precursor form of rat DMGDH complexed with tetrahydrofolate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

monomer

Ligands

1 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Covalent)

FAD.1: 35 residues within 4Å: Chain A: I.50, G.51, G.52, G.53, C.54, V.55, L.74, E.75, K.76, E.78, A.81, G.82, S.83, T.84, H.86, A.87, A.88, G.89, L.90, P.213, V.214, A.242, A.243, G.244, W.246, H.265, Y.267, G.365, P.366, I.367, F.392, Y.394, G.395, I.396, I.397 33 PLIP interactions: 33 interactions with chain A Hydrophobic interactions: A:Y.267, A:Y.267, A:I.367 Hydrogen bonds: A:G.52, A:G.53, A:V.55, A:K.76, A:A.81, A:G.82, A:S.83, A:S.83, A:T.84, A:T.84, A:A.88, A:G.89, A:L.90, A:L.90, A:V.214, A:V.214, A:F.392, A:G.395, A:I.396, A:I.397 Water bridges: A:G.52, A:G.56, A:S.77, A:S.77, A:T.80, A:S.83, A:G.244, A:G.244, A:F.245, A:F.245

1 x THG: (6S)-5,6,7,8-TETRAHYDROFOLATE(Non-covalent)

THG.2: 13 residues within 4Å: Chain A: F.532, I.562, E.575, T.577, I.589, F.651, L.652, Y.671, E.678, Y.680, F.719, Y.739, F.740 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:I.562, A:F.651 Hydrogen bonds: A:E.575, A:T.577, A:T.577, A:I.589, A:Y.671, A:Y.680 Salt bridges: A:E.678 pi-Stacking: A:Y.671, A:F.719

4 x SCN: THIOCYANATE ION(Non-functional Binders)

SCN.3: 5 residues within 4Å: Chain A: K.101, K.102, Y.105, A.153, T.154 1 PLIP interactions: 1 interactions with chain A Water bridges: A:A.153 SCN.4: 4 residues within 4Å: Chain A: P.379, Y.573, R.600, W.601 No protein-ligand interaction detected (PLIP) SCN.5: 4 residues within 4Å: Chain A: K.429, W.430, R.465, D.620 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:W.430 Water bridges: A:K.429, A:R.683 SCN.6: 2 residues within 4Å: Chain A: R.849, Q.853 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Luka, Z. et al., Folate in demethylation: The crystal structure of the rat dimethylglycine dehydrogenase complexed with tetrahydrofolate. Biochem.Biophys.Res.Commun. (2014)

Release Date

2014-06-18

Peptides

Dimethylglycine dehydrogenase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Dimethylglycine dehydrogenase

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