SMTL ID : 3zcz.1 (3 other biounits)

Crystal structure of a complex between Actinomadura R39 DD-peptidase and a trifluoroketone inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

monomer

Ligands

1 x TFR: (2R)-2-amino-7-oxo-7-{[(2R,3S)-4,4,4-trifluoro-3-hydroxybutan-2-yl]amino}heptanoic acid(Covalent)

TFR.1: 16 residues within 4Å: Chain A: A.48, S.49, K.52, W.139, D.142, Y.147, S.298, N.300, S.347, G.348, L.349, R.351, G.412, T.413, M.414, S.415 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:Y.147 Hydrogen bonds: A:S.49, A:D.142, A:N.300, A:T.413, A:T.413, A:T.413, A:S.415 Salt bridges: A:R.351 Halogen bonds: A:S.298

5 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 3 residues within 4Å: Chain A: D.281, H.282, T.283 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.281, A:T.283, A:T.283 Salt bridges: A:H.282 SO4.3: 3 residues within 4Å: Chain A: Y.145, A.234, R.236 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.235 Water bridges: A:R.236 Salt bridges: A:R.236 SO4.4: 4 residues within 4Å: Chain A: S.131, E.132, R.133, L.134 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.133, A:L.134 SO4.5: 4 residues within 4Å: Chain A: G.159, E.160, R.161 Ligands: MG.7 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.160, A:R.161 SO4.8: 4 residues within 4Å: Chain A: L.18, E.19, G.20, A.21 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.19, A:G.20, A:A.21

2 x MG: MAGNESIUM ION(Non-covalent)

MG.6: 3 residues within 4Å: Chain A: E.188, H.247, E.251 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.188, A:H.247, A:E.251 MG.7: 3 residues within 4Å: Chain A: H.158, E.168 Ligands: SO4.5 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:H.158, A:E.168

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dzhekieva, L. et al., Inhibition of Dd-Peptidases by a Specific Trifluoroketone: Crystal Structure of a Complex with the Actinomadura R39 Dd-Peptidase. Biochemistry (2013)

Release Date

2013-03-27

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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