SMTL ID : 1rcq.1

The 1.45 A crystal structure of alanine racemase from a pathogenic bacterium, Pseudomonas aeruginosa, contains both internal and external aldimine forms

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.45 Å

Oligo State

homo-dimer

Ligands

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

PLP.1: 17 residues within 4Å: Chain A: V.31, K.33, Y.37, L.78, K.122, R.129, M.156, H.158, N.192, S.193, P.194, R.208, P.209, G.210, I.211, Y.341 Ligands: DLY.2 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:V.31, A:V.31, A:K.33, A:L.78 Hydrogen bonds: A:K.33, A:R.129, A:N.192, A:S.193, A:R.208, A:R.208, A:G.210, A:I.211, A:Y.341 pi-Stacking: A:H.158 PLP.3: 17 residues within 4Å: Chain B: V.31, K.33, Y.37, L.78, K.122, R.129, M.156, H.158, N.192, S.193, P.194, R.208, P.209, G.210, I.211, Y.341 Ligands: DLY.4 14 PLIP interactions: 13 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:V.31, B:V.31, B:K.33, B:L.78 Hydrogen bonds: B:Y.37, B:R.129, B:N.192, B:S.193, B:R.208, B:R.208, B:G.210, B:I.211 pi-Stacking: B:H.158 Water bridges: A:Y.253

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

DLY.2: 12 residues within 4Å: Chain A: K.33, Y.37, R.129, H.158, Y.341 Chain B: Y.253, Y.272, S.300, M.301, D.302, M.303 Ligands: PLP.1 16 PLIP interactions: 9 interactions with chain A, 7 interactions with chain B Hydrophobic interactions: A:Y.341, B:Y.253, B:M.301 Hydrogen bonds: A:K.33, A:Y.37, A:R.129, A:R.129, B:Y.253, B:M.301, B:D.302, B:D.302, B:M.303 Water bridges: A:E.79, A:Y.341 Salt bridges: A:K.33, A:R.129 DLY.4: 12 residues within 4Å: Chain A: Y.253, Y.272, S.300, M.301, D.302, M.303 Chain B: K.33, Y.37, R.129, H.158, Y.341 Ligands: PLP.3 14 PLIP interactions: 8 interactions with chain B, 6 interactions with chain A Hydrophobic interactions: B:Y.341, A:Y.253, A:M.301 Hydrogen bonds: B:K.33, B:K.33, B:Y.37, B:R.129, B:R.129, A:M.301, A:D.302, A:M.303 Salt bridges: B:K.33, B:R.129 Water bridges: A:Y.253

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

LeMagueres, P. et al., Crystal structure at 1.45 A resolution of alanine racemase from a pathogenic bacterium, Pseudomonas aeruginosa, contains both internal and external aldimine forms. Biochemistry (2003)

Release Date

2004-06-01

Peptides

catabolic alanine racemase DadX: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

catabolic alanine racemase DadX