SMTL ID : 1scw.1

TOWARD BETTER ANTIBIOTICS: CRYSTAL STRUCTURE OF R61 DD-PEPTIDASE INHIBITED BY A NOVEL MONOCYCLIC PHOSPHATE INHIBITOR

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.13 Å

Oligo State

monomer

Ligands

1 x CP5: (2Z)-3-{[OXIDO(OXO)PHOSPHINO]OXY}-2-PHENYLACRYLATE(Covalent)

CP5.1: 11 residues within 4Å: Chain A: G.61, S.62, Y.159, R.285, H.298, T.299, G.300, T.301, V.302 Ligands: GOL.2, GOL.6 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:Y.159, A:Y.159 Hydrogen bonds: A:S.62, A:S.62, A:Y.159, A:T.299, A:T.301, A:V.302 Water bridges: A:K.65, A:N.161 Salt bridges: A:K.65, A:R.285, A:H.298 pi-Stacking: A:Y.159

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 6 residues within 4Å: Chain A: F.120, W.233, T.301, V.302, Q.303 Ligands: CP5.1 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:T.301, A:Q.303 Water bridges: A:F.120, A:T.123, A:N.161, A:T.301, A:S.326 GOL.3: 2 residues within 4Å: Chain A: T.175, H.177 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.177 GOL.4: 3 residues within 4Å: Chain A: E.172, V.179, H.200 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.172, A:H.200 Water bridges: A:Y.137, A:Y.198 GOL.5: 6 residues within 4Å: Chain A: N.192, L.193, T.194, Q.245, D.246, T.249 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:T.194, A:T.194, A:D.195, A:D.246, A:T.249, A:T.249 GOL.6: 5 residues within 4Å: Chain A: D.114, T.116, N.117, Y.159 Ligands: CP5.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.117, A:N.117 Water bridges: A:T.116 GOL.7: 6 residues within 4Å: Chain A: V.204, I.205, P.206, G.207, H.209, E.228 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.207, A:H.209, A:E.228

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Silvaggi, N.R. et al., Toward Better Antibiotics: Crystallographic Studies of a Novel Class of DD-Peptidase/beta-Lactamase Inhibitors. Biochemistry (2004)

Release Date

2004-06-22

Peptides

D-alanyl-D-alanine carboxypeptidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D-alanyl-D-alanine carboxypeptidase

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