SMTL ID : 5k50.3 (3 other biounits)

Three-dimensional structure of L-threonine 3-dehydrogenase from Trypanosoma brucei bound to NAD+ and L-allo-threonine refined to 2.23 angstroms

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.26 Å

Oligo State

homo-dimer

Ligands

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

NAD.1: 25 residues within 4Å: Chain A: G.7, L.9, G.10, Q.11, I.12, D.33, V.34, L.52, D.53, C.54, L.75, P.76, A.77, M.79, I.93, P.115, S.116, T.117, Y.142, K.146, L.169, P.170, G.171, I.172 Ligands: ALO.2 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:L.169 Hydrogen bonds: A:L.9, A:Q.11, A:Q.11, A:Q.11, A:I.12, A:V.34, A:D.53, A:C.54, A:L.55, A:L.75, A:K.146, A:I.172 Water bridges: A:G.7, A:G.10, A:G.13 NAD.5: 26 residues within 4Å: Chain B: G.7, L.9, G.10, Q.11, I.12, D.33, V.34, L.52, D.53, C.54, L.75, P.76, A.77, M.79, I.93, P.115, S.116, T.117, Y.142, K.146, L.169, P.170, I.172, G.180, T.184 Ligands: ALO.7 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:I.12, B:L.169 Hydrogen bonds: B:Q.11, B:Q.11, B:Q.11, B:I.12, B:V.34, B:D.53, B:C.54, B:L.75, B:K.146, B:I.172, B:G.180 Water bridges: B:G.10, B:G.13, B:T.184, B:T.184

2 x ALO: ALLO-THREONINE(Non-covalent)

ALO.2: 10 residues within 4Å: Chain A: M.79, S.80, T.117, I.118, Y.142, A.183, T.184, W.278 Ligands: NAD.1, ACT.3 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:I.118, A:W.278 Hydrogen bonds: A:S.80, A:Y.142, A:Y.142, A:A.183, A:T.184, A:T.184 ALO.7: 10 residues within 4Å: Chain B: M.79, S.80, T.117, I.118, Y.142, G.182, A.183, T.184, W.278 Ligands: NAD.5 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:I.118 Hydrogen bonds: B:S.80, B:Y.142, B:Y.142, B:Y.142, B:A.183, B:T.184, B:T.184 Water bridges: B:T.184

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

ACT.3: 7 residues within 4Å: Chain A: M.79, S.80, V.81, R.82, G.182, A.183 Ligands: ALO.2 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.80, A:V.81, A:R.82, A:A.183 ACT.4: 4 residues within 4Å: Chain A: R.157, T.234, R.235, T.236 3 PLIP interactions: 3 interactions with chain A Water bridges: A:T.236, A:T.236 Salt bridges: A:R.157

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 2 residues within 4Å: Chain B: E.265, V.267 No protein-ligand interaction detected (PLIP)

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
C

B
G

L-threonine 3-dehydrogenase

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