SMTL ID : 5k4q.1 (5 other biounits)

Three-dimensional structure of L-threonine 3-dehydrogenase from Trypanosoma brucei bound to NAD+ refined to 2.3 angstroms

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

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

NAD.1: 26 residues within 4Å: Chain A: G.8, L.10, G.11, Q.12, I.13, D.34, V.35, L.53, D.54, C.55, L.76, P.77, A.78, M.80, I.94, P.116, S.117, T.118, Y.143, K.147, L.170, P.171, G.172, I.173, T.185 Ligands: GOL.2 22 PLIP interactions: 22 interactions with chain A Hydrophobic interactions: A:L.170 Hydrogen bonds: A:G.8, A:L.10, A:Q.12, A:Q.12, A:Q.12, A:I.13, A:G.14, A:V.35, A:D.54, A:D.54, A:C.55, A:L.56, A:L.76, A:Y.143, A:K.147, A:I.173, A:T.185 Water bridges: A:G.8, A:G.8, A:G.11, A:Q.12 NAD.3: 24 residues within 4Å: Chain B: G.8, L.10, G.11, Q.12, I.13, D.34, V.35, L.53, D.54, C.55, L.76, P.77, A.78, M.80, I.94, P.116, S.117, T.118, Y.143, K.147, L.170, P.171, G.172, I.173 19 PLIP interactions: 19 interactions with chain B Hydrophobic interactions: B:L.170 Hydrogen bonds: B:G.8, B:L.10, B:Q.12, B:Q.12, B:Q.12, B:I.13, B:V.35, B:D.54, B:D.54, B:C.55, B:L.76, B:Y.143, B:K.147, B:I.173 Water bridges: B:G.11, B:Q.12, B:G.14, B:T.185

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 9 residues within 4Å: Chain A: M.80, S.81, V.82, T.118, Y.143, G.183, A.184, W.279 Ligands: NAD.1 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:S.81, A:V.82, A:T.118, A:T.118, A:A.184 Water bridges: A:G.183, A:D.186 GOL.4: 8 residues within 4Å: Chain B: M.80, S.81, V.82, R.83, Y.143, G.183, A.184, D.186 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:S.81, B:S.81, B:V.82, B:R.83, B:A.184, B:T.185, B:D.186 Water bridges: B:M.80

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

SO4.5: 3 residues within 4Å: Chain B: R.83, G.181, G.182 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.182

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

2017-11-15

Peptides

L-threonine 3-dehydrogenase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

L-threonine 3-dehydrogenase

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