SMTL ID : 5lc1.5 (5 other biounits)

L-threonine dehydrogenase from Trypanosoma brucei with NAD and the inhibitor pyruvate bound.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

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

NAD.1: 27 residues within 4Å: Chain A: G.9, L.11, G.12, Q.13, I.14, D.35, V.36, V.37, L.54, D.55, C.56, L.77, P.78, A.79, M.81, I.95, P.117, S.118, T.119, Y.144, K.148, L.171, P.172, G.173, I.174, G.182 Ligands: PYR.2 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:L.171 Hydrogen bonds: A:G.9, A:L.11, A:Q.13, A:Q.13, A:Q.13, A:I.14, A:G.15, A:V.36, A:D.55, A:C.56, A:L.57, A:L.77, A:K.148, A:I.174 Water bridges: A:G.12, A:P.181, A:G.182, A:G.182 NAD.4: 27 residues within 4Å: Chain B: G.9, L.11, G.12, Q.13, I.14, G.15, D.35, V.36, L.54, D.55, C.56, L.77, P.78, A.79, M.81, I.95, P.117, S.118, T.119, Y.144, K.148, L.171, P.172, G.173, I.174, G.182 Ligands: PYR.5 21 PLIP interactions: 21 interactions with chain B Hydrophobic interactions: B:I.14, B:L.171 Hydrogen bonds: B:G.9, B:L.11, B:Q.13, B:Q.13, B:Q.13, B:I.14, B:G.15, B:V.36, B:D.55, B:C.56, B:L.57, B:L.77, B:K.148, B:I.174 Water bridges: B:G.12, B:R.84, B:P.181, B:G.182, B:G.182

2 x PYR: PYRUVIC ACID(Non-covalent)

PYR.2: 11 residues within 4Å: Chain A: M.81, S.82, T.119, I.120, Y.144, G.173, G.184, A.185, T.186, W.280 Ligands: NAD.1 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:I.120 Hydrogen bonds: A:S.82, A:S.82, A:S.82, A:Y.144, A:A.185, A:T.186 PYR.5: 9 residues within 4Å: Chain B: M.81, S.82, T.119, Y.144, G.184, A.185, T.186, W.280 Ligands: NAD.4 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:W.280 Hydrogen bonds: B:S.82, B:S.82, B:T.119, B:Y.144, B:A.185, B:T.186

2 x NA: SODIUM ION(Non-functional Binders)

NA.3: 4 residues within 4Å: Chain A: K.129, E.210, S.211, D.282 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.129, A:S.211, A:D.282, A:D.282 NA.7: 6 residues within 4Å: Chain B: E.210, S.211, L.212, W.280, P.281, D.282 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.210, B:P.281, B:D.282

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.6: 6 residues within 4Å: Chain B: D.17, S.176, A.177, A.178, Y.216, M.217 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:M.217 Hydrogen bonds: B:D.17, B:A.177, B:A.178

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Adjogatse, E. et al., Structure and function of L-threonine-3-dehydrogenase from the parasitic protozoan Trypanosoma brucei revealed by X-ray crystallography and geometric simulations. Acta Crystallogr D Struct Biol (2018)

Release Date

2016-07-27

Peptides

L-threonine 3-dehydrogenase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
F

B
E

L-threonine 3-dehydrogenase

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