SMTL ID : 1pw1.1

Non-Covalent Complex Of Streptomyces R61 DD-Peptidase With A Highly Specific Penicillin

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.20 Å

Oligo State

monomer

Ligands

1 x HEL: (2S,5R,6R)-6-{[(6R)-6-(GLYCYLAMINO)-7-OXIDO-7-OXOHEPTANOYL]AMINO}-3,3-DIMETHYL-7-OXO-4-THIA-1-AZABICYCLO[3.2.0]HEPTANE-2-CARBOXYLATE(Non-covalent)

HEL.1: 18 residues within 4Å: Chain A: G.61, S.62, T.116, F.120, T.123, Y.159, N.161, L.214, W.233, R.285, H.298, T.299, G.300, T.301, Q.303, S.326, N.327 Ligands: FOR.5 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:F.120, A:Y.159, A:W.233, A:T.301 Hydrogen bonds: A:S.62, A:S.62, A:S.62, A:T.116, A:T.123, A:N.161, A:T.299, A:T.301, A:T.301, A:S.326, A:N.327 Water bridges: A:T.123, A:Y.159, A:T.301 Salt bridges: A:R.285, A:H.298

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 2 residues within 4Å: Chain A: K.80 Ligands: GOL.3 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.80, A:K.80 Water bridges: A:R.186, A:R.186 GOL.3: 4 residues within 4Å: Chain A: T.175, G.176, H.177 Ligands: GOL.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.176 Water bridges: A:L.174, A:T.175 GOL.4: 6 residues within 4Å: Chain A: V.204, I.205, P.206, G.207, H.209, E.228 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.207, A:H.209, A:E.228

2 x FOR: FORMYL GROUP(Covalent)

FOR.5: 7 residues within 4Å: Chain A: K.65, H.108, Y.159, R.285, H.298 Ligands: HEL.1, FOR.6 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:K.65, A:Y.159 FOR.6: 5 residues within 4Å: Chain A: K.65, H.108, Y.159, Y.280 Ligands: FOR.5 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:K.65, A:Y.159, A:Y.280

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Silvaggi, N.R. et al., Crystal structures of complexes between the R61 DD-peptidase and peptidoglycan-mimetic beta-lactams: a non-covalent complex with a "perfect penicillin. J.Mol.Biol. (2005)

Release Date

2004-07-13

Peptides

D-alanyl-D-alanine carboxypeptidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D-alanyl-D-alanine carboxypeptidase

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