SMTL ID : 4b4x.4 (3 other biounits)

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.65 Å

Oligo State

monomer

Ligands

1 x HQZ: trihydroxy{(1S)-1-[(methylsulfonyl)amino]ethyl}borate(1-)(Covalent)

HQZ.1: 8 residues within 4Å: Chain A: A.48, S.49, Y.147, S.298, N.300, L.349, G.412, T.413 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:S.49, A:S.298, A:N.300, A:T.413, A:T.413, A:T.413 Water bridges: A:S.298

6 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:T.283, A:T.283, A:T.283 Salt bridges: A:H.282 SO4.3: 2 residues within 4Å: Chain A: A.234, R.236 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.236 SO4.4: 4 residues within 4Å: Chain A: S.131, E.132, R.133, L.134 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.131, A:R.133, A:L.134 SO4.5: 3 residues within 4Å: Chain A: H.158, E.168 Ligands: SO4.8 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:H.158 SO4.8: 3 residues within 4Å: Chain A: H.158, G.159 Ligands: SO4.5 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.159 Water bridges: A:A.100 Salt bridges: A:H.158 SO4.9: 7 residues within 4Å: Chain A: D.95, T.97, L.98, D.102, H.282, S.284, A.285 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.97, A:D.102, A:A.285 Salt bridges: A:H.282

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: 2 residues within 4Å: Chain A: V.406, H.462 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.462

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sauvage, E., Crystal Structure of a Complex between Actinomadura R39 Dd-Peptidase and a Boronate Inhibitor. To be Published

Release Date

2013-08-21

Peptides

D-ALANYL-D-ALANINE CARBOXYPEPTIDASE: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

D-ALANYL-D-ALANINE CARBOXYPEPTIDASE

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