SMTL ID : 2xk1.1 (3 other biounits)

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

monomer

Ligands

1 x EWB: [(1S)-1-{[(2-benzylphenyl)carbonyl]amino}ethyl](trihydroxy)borate(1-)(Covalent)

EWB.1: 11 residues within 4Å: Chain A: A.48, S.49, K.52, Y.147, S.298, N.300, S.347, G.348, L.349, G.412, T.413 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:Y.147, A:L.349, A:T.413 Hydrogen bonds: A:S.49, A:S.298, A:N.300, A:T.413, A:T.413, A:T.413 pi-Stacking: A:Y.147

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

SO4.2: 3 residues within 4Å: Chain A: D.281, H.282, T.283 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.281, A:T.283 Salt bridges: A:H.282 SO4.3: 3 residues within 4Å: Chain A: A.234, L.235, R.236 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.235 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: 3 residues within 4Å: Chain A: G.159, E.160, R.161 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.159, A:E.160, A:R.161

2 x CO: COBALT (II) ION(Non-covalent)

CO.6: 3 residues within 4Å: Chain A: E.188, H.247, E.251 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.188, A:H.247, A:E.251, A:E.251 CO.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

Woon, E.C.Y. et al., Structure Guided Development of Potent Reversibly Binding Penicillin Binding Protein Inhibitors. Acs Med.Chem.Lett. (2011)

Release Date

2011-01-26

Peptides

D-ALANYL-D-ALANINE CARBOXYPEPTIDASE: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D-ALANYL-D-ALANINE CARBOXYPEPTIDASE

Related Entries With Identical Sequence