SMTL ID : 4v15.1

Crystal structure of D-threonine aldolase from Alcaligenes xylosoxidans

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

homo-dimer

Ligands

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

PLP.1: 15 residues within 4Å: Chain A: H.57, K.59, Q.81, R.157, Q.185, Y.187, G.231, G.232, T.233, Q.249, A.250, G.251, S.252, Y.260 Ligands: PLP.2 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:Y.187 Hydrogen bonds: A:Q.81, A:R.157, A:Y.187, A:T.233, A:T.233, A:G.251, A:S.252 Water bridges: A:K.59, A:K.59, A:K.59, A:K.59, A:S.252 Salt bridges: A:K.59 pi-Stacking: A:H.57, A:Y.187 PLP.2: 16 residues within 4Å: Chain A: H.57, K.59, Q.81, S.100, R.157, Q.185, Y.187, G.231, G.232, T.233, Q.249, A.250, G.251, S.252, Y.260 Ligands: PLP.1 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:K.59, A:Q.81, A:Q.81, A:R.157, A:Y.187, A:T.233, A:T.233, A:G.251, A:S.252, A:Y.260 Water bridges: A:R.157, A:R.157, A:S.252 Salt bridges: A:K.59 pi-Stacking: A:H.57, A:Y.187 PLP.5: 15 residues within 4Å: Chain B: H.57, K.59, Q.81, R.157, Q.185, Y.187, G.231, G.232, T.233, Q.249, A.250, G.251, S.252, Y.260 Ligands: PLP.6 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:K.59, B:Y.187 Hydrogen bonds: B:Q.81, B:R.157, B:T.233, B:G.251, B:S.252, B:Y.260 Water bridges: B:K.59, B:K.59, B:R.157, B:Y.187, B:Y.187, B:S.252, B:D.349 pi-Stacking: B:Y.187 pi-Cation interactions: B:H.57 PLP.6: 16 residues within 4Å: Chain B: H.57, K.59, Q.81, S.100, R.157, Q.185, Y.187, G.231, G.232, T.233, Q.249, A.250, G.251, S.252, Y.260 Ligands: PLP.5 15 PLIP interactions: 15 interactions with chain B Hydrogen bonds: B:Q.81, B:R.157, B:Y.187, B:T.233, B:G.251, B:S.252, B:Y.260 Water bridges: B:K.59, B:K.59, B:K.59, B:R.157, B:S.252, B:S.252 pi-Stacking: B:H.57, B:Y.187

2 x MN: MANGANESE (II) ION(Non-covalent)

MN.3: 2 residues within 4Å: Chain A: H.347, D.349 6 PLIP interactions: 2 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:H.347, A:D.349, H2O.5, H2O.15, H2O.19, H2O.19 MN.7: 2 residues within 4Å: Chain B: H.347, D.349 6 PLIP interactions: 2 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:H.347, B:D.349, H2O.18, H2O.25, H2O.33, H2O.36

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

NA.4: 5 residues within 4Å: Chain A: A.173, R.174, A.175, L.176, L.179 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.173 Water bridges: A:G.178 NA.8: 4 residues within 4Å: Chain B: A.173, R.174, L.176, L.179 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:L.179 Water bridges: B:N.180

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Uhl, M.K. et al., The Crystal Structure of D-Threonine Aldolase from Alcaligenes Xylosoxidans Provides Insight Into a Metal Ion Assisted Plp-Dependent Mechanism. Plos One (2015)

Release Date

2015-03-25

Peptides

D-THREONINE ALDOLASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

D-THREONINE ALDOLASE