SMTL ID : 3giq.2 (1 other biounit)

Crystal structure of N-acyl-D-Glutamate Deacylase from Bordetella Bronchiseptica complexed with zinc and phosphonate inhibitor, a mimic of the reaction tetrahedral intermediate.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

monomer

Ligands

1 x G01: N-[(R)-hydroxy(methyl)phosphoryl]-D-glutamic acid(Non-covalent)

G01.1: 20 residues within 4Å: Chain A: H.66, H.68, C.95, L.114, Y.190, H.218, E.222, H.248, K.250, M.252, Y.282, S.287, S.288, T.289, R.295, Y.343, D.365, R.376 Ligands: ZN.2, ZN.3 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:T.289 Hydrogen bonds: A:Y.190, A:Y.282, A:S.287, A:S.288, A:D.365, A:D.365, A:R.376 Water bridges: A:H.218, A:E.222 Salt bridges: A:H.248, A:K.250, A:R.295, A:R.376

2 x ZN: ZINC ION(Non-covalent)

ZN.2: 5 residues within 4Å: Chain A: C.95, H.218, H.248 Ligands: G01.1, ZN.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.95, A:H.218, A:H.248 ZN.3: 6 residues within 4Å: Chain A: H.66, H.68, C.95, D.365 Ligands: G01.1, ZN.2 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.66, A:H.68, A:C.95, A:D.365

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cummings, J.A. et al., Annotating enzymes of uncertain function: the deacylation of D-amino acids by members of the amidohydrolase superfamily. Biochemistry (2009)

Release Date

2009-09-01

Peptides

N-acyl-D-glutamate deacylase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

N-acyl-D-glutamate deacylase

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