SMTL ID : 3a9w.1

Crystal structure of L-Threonine bound L-Threonine dehydrogenase (Y137F) from Hyperthermophilic Archaeon Thermoplasma volcanium

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-dimer

Ligands

2 x THR: THREONINE(Non-covalent)

THR.1: 9 residues within 4Å: Chain A: L.73, S.74, T.112, F.137, G.177, T.178, T.179, W.273 Ligands: NAD.2 10 PLIP interactions: 8 interactions with chain A, 2 Ligand-Ligand interactions Hydrophobic interactions: A:W.273 Hydrogen bonds: A:S.74, A:S.74, A:T.178, A:T.179, T.1, T.1 Water bridges: A:Q.10, A:I.167, A:T.179 THR.4: 10 residues within 4Å: Chain B: L.73, S.74, T.112, F.137, P.165, G.166, T.178, T.179, W.273 Ligands: NAD.5 11 PLIP interactions: 9 interactions with chain B, 2 Ligand-Ligand interactions Hydrogen bonds: B:S.74, B:T.112, B:T.178, B:T.179, T.4, T.4 Water bridges: B:A.75, B:I.113, B:T.178, B:D.180, B:D.180

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

NAD.2: 26 residues within 4Å: Chain A: G.6, S.8, G.9, Q.10, I.11, D.32, I.33, V.34, L.46, D.47, V.48, L.69, A.70, G.71, L.73, V.87, P.110, S.111, T.112, F.137, K.141, Y.164, P.165, G.166, I.167 Ligands: THR.1 19 PLIP interactions: 17 interactions with chain A, 2 Ligand-Ligand interactions Hydrophobic interactions: A:Y.164, T.1 Hydrogen bonds: 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:K.141, A:I.167, T.1 Water bridges: A:G.6, A:G.9, A:G.12, A:K.141 pi-Stacking: A:Y.164 NAD.5: 24 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, L.69, A.70, G.71, L.73, V.87, P.110, S.111, T.112, F.137, K.141, Y.164, P.165, I.167 Ligands: THR.4 21 PLIP interactions: 19 interactions with chain B, 2 Ligand-Ligand interactions Hydrophobic interactions: B:Y.164, T.4 Hydrogen bonds: B:S.8, B:S.8, B:Q.10, B:Q.10, B:I.11, B:I.33, B:D.47, B:D.47, B:V.48, B:L.69, B:K.141, B:I.167, T.4 Water bridges: B:G.6, B:G.9, B:I.72, B:K.141, B:T.179 pi-Stacking: B:Y.164

1 x MRD: (4R)-2-METHYLPENTANE-2,4-DIOL(Non-functional Binders)

MRD.3: 3 residues within 4Å: Chain A: E.173, Y.187, Y.188 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:E.173, A:Y.187, A:Y.187, A:Y.187, A:Y.188

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

MPD.6: 4 residues within 4Å: Chain A: E.153, K.154 Chain B: R.134, K.268 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:K.268 Hydrophobic interactions: A:E.153

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

2010-11-10

Peptides

NDP-sugar epimerase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

NDP-sugar epimerase

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