SMTL ID : 1mpl.1

CRYSTAL STRUCTURE OF PHOSPHONATE-INHIBITED D-ALA-D-ALA PEPTIDASE REVEALS AN ANALOG OF A TETRAHEDRAL TRANSITION STATE

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.12 Å

Oligo State

monomer

Ligands

1 x RE1: GLYCYL-L-A-AMINOPIMELYL-E-(D-2-AMINOETHYL)PHOSPHONATE(Covalent)

RE1.1: 17 residues within 4Å: Chain A: G.61, S.62, F.120, T.123, Y.159, N.161, L.214, W.233, A.237, G.300, T.301, V.302, Q.303, S.326, N.327 Ligands: GOL.2, GOL.3 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:F.120, A:T.301 Hydrogen bonds: A:S.62, A:T.123, A:Y.159, A:N.161, A:T.301, A:T.301, A:T.301, A:S.326, A:N.327 Water bridges: A:T.123, A:T.301

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 4 residues within 4Å: Chain A: Y.306, N.327, V.329 Ligands: RE1.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.306, A:N.327 GOL.3: 5 residues within 4Å: Chain A: D.114, N.117, Y.159, N.161 Ligands: RE1.1 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.114, A:N.117, A:N.117, A:S.158 Water bridges: A:Y.159 GOL.4: 3 residues within 4Å: Chain A: E.172, V.179, H.200 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.172, A:H.200 Water bridges: A:Y.137, A:V.179, A:Y.198 GOL.5: 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 GOL.6: 5 residues within 4Å: Chain A: A.5, P.6, D.7, D.8, K.346 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:P.6, A:D.8 Water bridges: A:K.346, A:K.346

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Silvaggi, N.R. et al., The Crystal Structure of Phosphonate-Inhibited d-Ala-d-Ala Peptidase Reveals an Analogue of a Tetrahedral Transition State. Biochemistry (2003)

Release Date

2003-02-25

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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