SMTL ID : 6a2f.1

Crystal structure of biosynthetic alanine racemase from Pseudomonas aeruginosa

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-dimer

Ligands

2 x MLI: MALONATE ION(Non-functional Binders)

MLI.1: 7 residues within 4Å: Chain A: K.123, M.128, R.130, L.131, H.159 Chain B: M.304 Ligands: DLY.4 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:H.159 Hydrogen bonds: A:R.130, A:L.131, A:L.131 Salt bridges: A:K.123, A:R.130 MLI.6: 8 residues within 4Å: Chain A: M.304 Chain B: K.34, K.123, M.128, R.130, L.131, H.159 Ligands: DLY.2 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:H.159 Hydrogen bonds: B:R.130, B:L.131 Salt bridges: B:K.123, B:R.130

2 x DLY: D-LYSINE(Non-covalent)

DLY.2: 11 residues within 4Å: Chain A: Y.254, Y.273, S.301, M.302, D.303, M.304 Chain B: K.34, R.130, Y.342 Ligands: ACT.3, MLI.6 10 PLIP interactions: 9 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:Y.254, A:M.302 Hydrogen bonds: A:Y.273, A:S.301, A:S.301, A:S.301, A:M.302, A:D.303, A:M.304, B:R.130 DLY.4: 11 residues within 4Å: Chain A: K.34, R.130, Y.342 Chain B: Y.254, Y.273, S.301, M.302, D.303, M.304 Ligands: MLI.1, ACT.5 11 PLIP interactions: 2 interactions with chain A, 9 interactions with chain B Hydrogen bonds: A:R.130, B:Y.254, B:S.301, B:S.301, B:M.302, B:D.303, B:D.303, B:M.304 Water bridges: A:E.80 Hydrophobic interactions: B:Y.254, B:M.302

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.3: 5 residues within 4Å: Chain A: Y.254, R.279, R.299 Chain B: L.340 Ligands: DLY.2 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:L.340, A:Y.254 Hydrogen bonds: A:R.299 Salt bridges: A:R.279 ACT.5: 8 residues within 4Å: Chain A: L.340, Y.342 Chain B: Y.254, Y.273, R.279, R.299, V.300 Ligands: DLY.4 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:L.340, B:Y.254 Salt bridges: B:R.279

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dong, H. et al., Enzymatic characterization and crystal structure of biosynthetic alanine racemase from Pseudomonas aeruginosa PAO1. Biochem.Biophys.Res.Commun. (2018)

Release Date

2018-08-08

Peptides

Alanine racemase, biosynthetic: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Alanine racemase, biosynthetic