SMTL ID : 3a4v.1

Crystal structure of pyruvate bound L-Threonine dehydrogenase from Hyperthermophilic Archaeon Thermoplasma volcanium

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.78 Å

Oligo State

homo-dimer

Ligands

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

NAD.1: 25 residues within 4Å: Chain A: G.6, S.8, G.9, Q.10, I.11, D.32, I.33, L.46, D.47, V.48, L.69, A.70, G.71, L.73, V.87, P.110, S.111, T.112, Y.137, K.141, Y.164, P.165, G.166, I.167 Ligands: PYR.2 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:Y.164 Hydrogen bonds: A:G.6, A:S.8, A:S.8, A:Q.10, A:Q.10, A:I.11, A:I.33, A:D.47, A:V.48, A:L.69, A:G.71, A:Y.137, A:K.141, A:I.167, A:T.179 Water bridges: A:G.9, A:G.12 pi-Stacking: A:Y.164 NAD.4: 26 residues within 4Å: Chain B: G.6, S.8, G.9, Q.10, I.11, D.32, I.33, L.46, D.47, V.48, S.49, L.69, A.70, G.71, L.73, V.87, P.110, S.111, T.112, Y.137, K.141, Y.164, P.165, G.166, I.167 Ligands: PYR.5 19 PLIP interactions: 19 interactions with chain B Hydrophobic interactions: B:Y.164 Hydrogen bonds: B:G.6, B:Q.10, B:Q.10, B:I.11, B:I.33, B:D.47, B:D.47, B:V.48, B:S.49, B:L.69, B:G.71, B:K.141, B:I.167 Water bridges: B:G.9, B:G.12, B:I.72, B:K.141, B:T.179

2 x PYR: PYRUVIC ACID(Non-covalent)

PYR.2: 8 residues within 4Å: Chain A: L.73, S.74, T.112, Y.137, T.178, T.179, W.273 Ligands: NAD.1 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:T.179, A:W.273 Hydrogen bonds: A:S.74, A:S.74, A:S.74, A:T.178, A:T.178, A:T.179 PYR.5: 10 residues within 4Å: Chain B: L.73, S.74, T.112, Y.137, P.165, G.166, T.178, T.179, W.273 Ligands: NAD.4 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:T.179, B:W.273 Hydrogen bonds: B:S.74, B:S.74, B:S.74, B:T.112, B:Y.137, B:T.179 Water bridges: B:A.75, B:T.178

2 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.3: 4 residues within 4Å: Chain A: E.173, V.183, E.184, Y.187 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:E.173, A:E.173, A:V.183, A:E.184, A:Y.187, A:Y.187 MPD.6: 5 residues within 4Å: Chain A: E.153, K.154 Chain B: R.134, T.135, K.268 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:T.135, B:K.268, A:K.154

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yoneda, K. et al., Crystal Structure of Binary and Ternary Complexes of Archaeal UDP-galactose 4-Epimerase-like L-Threonine Dehydrogenase from Thermoplasma volcanium. J.Biol.Chem. (2012)

Release Date

2010-07-28

Peptides

NDP-sugar epimerase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

NDP-sugar epimerase

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