SMTL ID : 4muq.1

Crystal Structure of Vancomycin Resistance D,D-dipeptidase VanXYg in complex with D-Ala-D-Ala phosphinate analog

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.36 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: H.108, D.115, H.168 Ligands: LY0.2, 2D8.3 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.108, A:D.115, A:D.115, A:H.168

1 x LY0: (2R)-3-[(R)-[(1R)-1-aminoethyl](hydroxy)phosphoryl]-2-methylpropanoic acid(Non-covalent)

LY0.2: 16 residues within 4Å: Chain A: R.75, Q.80, Y.99, V.100, A.101, S.106, H.108, D.115, I.126, Y.152, I.162, E.165, W.167, H.168 Ligands: ZN.1, 2D8.3 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:A.101, A:Y.152, A:I.162 Hydrogen bonds: A:R.75, A:R.75, A:Q.80, A:A.101, A:W.167 Water bridges: A:S.106, A:E.107 Salt bridges: A:R.75, A:H.108

1 x 2D8: (2R)-3-[(R)-[(1S)-1-aminoethyl](hydroxy)phosphoryl]-2-methylpropanoic acid(Non-covalent)

2D8.3: 17 residues within 4Å: Chain A: R.75, Q.80, Y.99, V.100, A.101, S.106, H.108, D.115, F.125, I.126, Y.152, I.162, E.165, W.167, H.168 Ligands: ZN.1, LY0.2 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:A.101, A:Y.152, A:I.162 Hydrogen bonds: A:R.75, A:R.75, A:Q.80, A:A.101, A:E.165, A:W.167 Water bridges: A:S.106, A:E.107 Salt bridges: A:R.75, A:H.108

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.4: 5 residues within 4Å: Chain A: K.98, E.157, G.161, I.162, S.163 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.98, A:S.163

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 2 residues within 4Å: Chain A: R.154, D.155 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.154, A:R.154, A:D.155 Water bridges: A:D.155 GOL.6: 2 residues within 4Å: Chain A: N.66, S.67 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.66, A:N.66

4 x PE3: 3,6,9,12,15,18,21,24,27,30,33,36,39-TRIDECAOXAHENTETRACONTANE-1,41-DIOL(Non-functional Binders)

PE3.7: 7 residues within 4Å: Chain A: N.22, K.23, N.24, E.158, I.159, T.160, G.161 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.22, A:K.23, A:N.24, A:N.24, A:N.24 PE3.8: 4 residues within 4Å: Chain A: V.234, Y.235, Q.236, W.250 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.235 Water bridges: A:Y.235 PE3.9: 7 residues within 4Å: Chain A: L.88, K.89, D.90, N.91, G.92, E.93, D.94 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.89, A:E.93, A:D.94, A:D.94 Water bridges: A:F.95 PE3.10: 3 residues within 4Å: Chain A: K.33, G.34, R.49 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.34, A:R.49 Water bridges: A:L.35

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Meziane-Cherif, D. et al., Structural basis for the evolution of vancomycin resistance D,D-peptidases. Proc.Natl.Acad.Sci.USA (2014)

Release Date

2013-10-09

Peptides

D,D-dipeptidase/D,D-carboxypeptidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D,D-dipeptidase/D,D-carboxypeptidase

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