SMTL ID : 2y55.4 (3 other biounits)

Unexpected tricovalent binding mode of boronic acids within the active site of a penicillin binding protein

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

monomer

Ligands

1 x FP5: PHENYLACETAMIDOMETHYL BORONIC ACID(Covalent)

FP5.1: 11 residues within 4Å: Chain A: S.49, K.52, S.298, N.300, L.349, K.410, T.411, G.412, T.413, M.414 Ligands: ACN.8 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.349 Hydrogen bonds: A:T.413

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:T.283, A:T.283 Salt bridges: A:H.282 SO4.3: 2 residues within 4Å: Chain A: A.234, 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: 4 residues within 4Å: Chain A: H.158, G.159, E.160, R.161 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.160, A:E.160, A:E.160, A:R.161 Salt bridges: A:H.158

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

2 x ACN: ACETONE(Non-covalent)

ACN.8: 6 residues within 4Å: Chain A: D.142, Y.147, L.349, T.413, M.414 Ligands: FP5.1 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.147, A:L.349, A:M.414 ACN.9: 4 residues within 4Å: Chain A: T.127, W.128, F.129, G.318 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zervosen, A. et al., Unexpected Tricovalent Binding Mode of Boronic Acids within the Active Site of a Penicillin- Binding Protein. J.Am.Chem.Soc. (2011)

Release Date

2011-07-27

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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