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

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

monomer

Ligands

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

SO4.1: 7 residues within 4Å: Chain A: S.49, S.298, T.393, K.410, T.411, G.412, T.413 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:S.49, A:S.49, A:S.298, A:T.411, A:T.413 Water bridges: A:S.49, A:G.412, A:G.412 Salt bridges: A:K.410 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 4 PLIP interactions: 4 interactions with chain A Water bridges: A:L.235, A:L.235, A:R.236 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: 4 residues within 4Å: Chain A: H.158, G.159, E.160, R.161 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:E.160, A:E.160, A:E.160, A:R.161 Water bridges: A:H.158 Salt bridges: 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 No protein-ligand interaction detected (PLIP)

1 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.8: 8 residues within 4Å: Chain A: G.368, A.373, Q.374, W.376, S.377, E.408, Y.423, E.430 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.374 Salt bridges: A:E.430

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dzhekieva, L. et al., Crystal Structure of a Complex between the Actinomadura R39 Dd-Peptidase and a Peptidoglycan- Mimetic Boronate Inhibitor: Interpretation of a Transition State Analogue in Terms of Catalytic Mechanism. Biochemistry (2010)

Release Date

2010-07-21

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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