SMTL ID : 5k4w.1

Three-dimensional structure of L-threonine 3-dehydrogenase from Trypanosoma brucei bound to NADH and L-threonine refined to 1.72 angstroms

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.72 Å

Oligo State

homo-dimer

Ligands

2 x NAI: 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE(Non-covalent)

NAI.1: 26 residues within 4Å: Chain A: G.9, L.11, G.12, Q.13, I.14, 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: THR.2 22 PLIP interactions: 20 interactions with chain A, 2 Ligand-Ligand interactions Hydrophobic interactions: A:L.171, T.2 Hydrogen bonds: A:L.11, A:Q.13, A:Q.13, A:Q.13, A:I.14, A:V.36, A:D.55, A:D.55, A:C.56, A:L.77, A:Y.144, A:K.148, A:I.174, T.2 Water bridges: A:G.9, A:G.12, A:G.15, A:P.181, A:G.182, A:G.182 NAI.5: 27 residues within 4Å: Chain B: 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: THR.6 25 PLIP interactions: 23 interactions with chain B, 2 Ligand-Ligand interactions Hydrophobic interactions: B:L.171, T.6 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:D.55, B:C.56, B:L.77, B:Y.144, B:K.148, B:I.174, T.6 Water bridges: B:G.12, B:R.84, B:P.181, B:G.182, B:T.186, B:T.186, B:T.186

2 x THR: THREONINE(Non-covalent)

THR.2: 9 residues within 4Å: Chain A: M.81, S.82, T.119, Y.144, G.184, A.185, T.186, W.280 Ligands: NAI.1 9 PLIP interactions: 8 interactions with chain A, 1 Ligand-Ligand interactions Hydrogen bonds: A:S.82, A:T.119, A:Y.144, A:A.185, A:T.186, A:T.186, T.2 Water bridges: A:T.186, A:D.187 THR.6: 9 residues within 4Å: Chain B: M.81, S.82, T.119, Y.144, G.184, A.185, T.186, W.280 Ligands: NAI.5 11 PLIP interactions: 2 Ligand-Ligand interactions, 9 interactions with chain B Hydrogen bonds: T.6, T.6, B:S.82, B:S.82, B:T.119, B:Y.144, B:A.185, B:T.186 Water bridges: B:T.186, B:T.186, B:D.187

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 5 residues within 4Å: Chain A: D.17, S.176, A.177, A.178, Y.216 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:A.177, A:A.178, A:Y.216, A:Y.216, A:Q.311 Water bridges: A:T.179 GOL.7: 7 residues within 4Å: Chain B: D.17, S.176, A.177, A.178, Y.216, M.217, M.308 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:A.177, B:A.178, B:Y.216, B:Y.216 Water bridges: B:D.17, B:T.179 GOL.8: 6 residues within 4Å: Chain B: M.2, R.23, D.24, K.25, F.26, G.27 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.23, B:K.25

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

NA.4: 7 residues within 4Å: Chain A: E.210, S.211, L.212, A.277, W.280, P.281, D.282 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.277 NA.9: 8 residues within 4Å: Chain B: K.129, E.210, S.211, L.212, A.277, W.280, P.281, D.282 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.129, B:E.210, B:P.281

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

2018-01-10

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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