SMTL ID : 3wqe.1

D-threo-3-hydroxyaspartate dehydratase from Delftia sp. HT23 complexed with D-allothreonine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-dimer

Ligands

2 x PLP: PYRIDOXAL-5'-PHOSPHATE(Non-covalent)

PLP.1: 15 residues within 4Å: Chain A: H.51, K.53, A.94, R.151, H.182, Y.187, G.226, S.227, T.228, P.229, R.244, A.245, G.246, V.247 Ligands: 2TL.3 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:H.182 Hydrogen bonds: A:R.151, A:R.151, A:Y.187, A:T.228, A:R.244, A:G.246, A:V.247 Water bridges: A:K.53 Salt bridges: A:K.53 pi-Stacking: A:H.51, A:H.182 PLP.4: 15 residues within 4Å: Chain B: H.51, K.53, A.94, R.151, H.182, Y.187, G.226, S.227, T.228, P.229, R.244, A.245, G.246, V.247 Ligands: 2TL.6 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:A.94 Hydrogen bonds: B:R.151, B:R.151, B:T.228, B:T.228, B:R.244, B:G.246, B:V.247 Water bridges: B:K.53, B:Y.187 Salt bridges: B:K.53, B:H.182 pi-Stacking: B:H.51, B:H.182

3 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: K.53, H.361, C.363 6 PLIP interactions: 2 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:H.361, A:C.363, H2O.7, H2O.9, H2O.9, H2O.18 MG.5: 3 residues within 4Å: Chain B: K.53, H.361, C.363 6 PLIP interactions: 2 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:H.361, B:C.363, H2O.5, H2O.18, H2O.18, H2O.18 MG.7: 1 residues within 4Å: Chain B: W.390 No protein-ligand interaction detected (PLIP)

2 x 2TL: D-allothreonine(Non-covalent)

2TL.3: 8 residues within 4Å: Chain A: K.53, H.150, R.151, H.182, Y.187 Chain B: N.328, Q.329 Ligands: PLP.1 12 PLIP interactions: 8 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:K.53, A:R.151, B:Q.329 Water bridges: A:H.51, A:K.53, A:R.151, A:Y.187, B:W.290, B:N.328, B:H.331 Salt bridges: A:K.53, A:R.151 2TL.6: 8 residues within 4Å: Chain A: N.328, Q.329 Chain B: K.53, H.150, R.151, H.182, Y.187 Ligands: PLP.4 12 PLIP interactions: 9 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:K.53, B:R.151, B:Y.187, A:Q.329 Water bridges: B:K.53, B:R.151, B:R.151, B:H.361, A:W.290, A:N.328 Salt bridges: B:K.53, B:R.151

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Matsumoto, Y. et al., Structural insights into the substrate stereospecificity of D-threo-3-hydroxyaspartate dehydratase from Delftia sp. HT23: a useful enzyme for the synthesis of optically pure L-threo- and D-erythro-3-hydroxyaspartate. Appl.Microbiol.Biotechnol. (2015)

Release Date

2015-01-28

Peptides

D-threo-3-hydroxyaspartate dehydratase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

D-threo-3-hydroxyaspartate dehydratase

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