SMTL ID : 3wqc.1

D-threo-3-hydroxyaspartate dehydratase from Delftia sp. HT23

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

homo-dimer

Ligands

2 x PLP: PYRIDOXAL-5'-PHOSPHATE(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: GOL.4 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:K.53, A:A.94, A:H.182 Hydrogen bonds: A:R.151, A:Y.187, A:T.228, A:R.244, A:G.246, A:V.247 pi-Stacking: A:H.182 PLP.8: 14 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 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:K.53, B:A.94, B:H.182 Hydrogen bonds: B:K.53, B:R.151, B:T.228, B:T.228, B:R.244, B:G.246, B:V.247 Water bridges: B:H.51, B:A.94, B:Y.187, B:Y.187, B:Y.187 Salt bridges: B:K.53, B:H.182 pi-Stacking: B:H.182

5 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: 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.3, H2O.3, H2O.8, H2O.16 MG.6: 1 residues within 4Å: Chain A: W.390 No protein-ligand interaction detected (PLIP) MG.9: 2 residues within 4Å: Chain B: 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.3, H2O.16, H2O.16, H2O.21 MG.11: 1 residues within 4Å: Chain A: D.146 No protein-ligand interaction detected (PLIP) MG.12: 1 residues within 4Å: Chain B: W.390 No protein-ligand interaction detected (PLIP)

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 6 residues within 4Å: Chain A: Y.187, V.254, G.298, R.301, Q.302 Chain B: R.295 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:Y.187, A:R.301, B:R.295 Water bridges: A:G.298, A:Q.302, B:R.295 GOL.4: 9 residues within 4Å: Chain A: K.53, H.150, R.151, H.182, G.184, Y.187 Chain B: N.328 Ligands: PLP.1, CL.7 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.53, A:K.53, A:R.151, A:H.182 Water bridges: A:R.151 GOL.10: 5 residues within 4Å: Chain A: R.295 Chain B: Y.187, G.298, R.301, Q.302 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:R.301, A:R.295 Water bridges: B:E.188, B:G.298, B:Q.302, A:R.295

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.5: 3 residues within 4Å: Chain A: N.328, Q.329 Chain B: K.53 Ligand excluded by PLIP CL.7: 5 residues within 4Å: Chain A: K.53, R.151 Chain B: N.328, Q.329 Ligands: GOL.4 Ligand excluded by PLIP

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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