SMTL ID : 2wke.2 (3 other biounits)

Crystal structure of the Actinomadura R39 DD-peptidase inhibited by 6- beta-iodopenicillanate.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

monomer

Ligands

1 x BIY: (3S)-2,2-dimethyl-3,4-dihydro-2H-1,4-thiazine-3,6-dicarboxylic acid(Covalent)

BIY.1: 8 residues within 4Å: Chain A: A.48, S.49, K.52, Y.147, S.298, N.300, G.412, T.413 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Y.147 Hydrogen bonds: A:S.49, A:T.413 Water bridges: A:K.410, A:T.413

5 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: 3 residues within 4Å: Chain A: A.234, L.235, 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: 2 residues within 4Å: Chain A: W.139, S.415 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.415, A:S.415 Water bridges: A:R.351 SO4.5: 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 SO4.6: 5 residues within 4Å: Chain A: T.97, D.102, H.282, T.283, S.284 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.95, A:A.285 Water bridges: A:T.97, A:T.97 Salt bridges: A:H.282

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

CO.7: 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 CO.8: 2 residues within 4Å: Chain A: L.63, H.67 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:L.63, A:H.67 CO.9: 2 residues within 4Å: Chain A: H.158, E.168 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.158

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sauvage, E. et al., Structural Basis of the Inhibition of Class a Beta-Lactamases and Penicillin-Binding Proteins by 6-Beta-Iodopenicillanate. J.Am.Chem.Soc. (2009)

Release Date

2009-12-01

Peptides

D-ALANYL-D-ALANINE CARBOXYPEPTIDASE: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

D-ALANYL-D-ALANINE CARBOXYPEPTIDASE

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