SMTL ID : 6qkb.1

Crystal structure of the beta-hydroxyaspartate aldolase of Paracoccus denitrificans

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-dimer

Ligands

2 x PLP: PYRIDOXAL-5'-PHOSPHATE(Covalent)

PLP.1: 15 residues within 4Å: Chain A: H.60, K.62, Q.85, T.104, R.162, Q.190, Y.192, G.236, G.237, T.238, Q.254, C.255, G.256, S.257, Y.265 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:K.62, A:Y.192 Hydrogen bonds: A:Q.85, A:Q.85, A:R.162, A:Y.192, A:T.238, A:T.238, A:G.256, A:S.257 Water bridges: A:K.62, A:Y.192, A:S.257, A:S.257, A:Y.265, A:D.357 pi-Stacking: A:Y.192 pi-Cation interactions: A:H.60 PLP.3: 15 residues within 4Å: Chain B: H.60, K.62, Q.85, T.104, R.162, Q.190, Y.192, G.236, G.237, T.238, Q.254, C.255, G.256, S.257, Y.265 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:K.62, B:Y.192 Hydrogen bonds: B:Q.85, B:R.162, B:T.238, B:T.238, B:G.256, B:S.257 Water bridges: B:Y.192, B:Y.192, B:S.257, B:D.357, B:D.357 pi-Stacking: B:Y.192 pi-Cation interactions: B:H.60

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: H.355, D.357 Chain B: D.331 6 PLIP interactions: 2 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:H.355, A:D.357, H2O.1, H2O.5, H2O.12, H2O.15 MG.4: 3 residues within 4Å: Chain A: D.331 Chain B: H.355, D.357 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:D.357, H2O.1, H2O.15, H2O.23, H2O.28

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schada von Borzyskowski, L. et al., Marine Proteobacteria metabolize glycolate via the beta-hydroxyaspartate cycle. Nature (2019)

Release Date

2019-08-14

Peptides

D-3-hydroxyaspartate aldolase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

D-3-hydroxyaspartate aldolase