SMTL ID : 4mus.1

Crystal structure of vancomycin resistance D,D-dipeptidase/D,D-pentapeptidase VanXYc D59S mutant in complex with D-Ala-D-Ala phosphinate analog

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.68 Å

Oligo State

homo-dimer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: H.116, D.123, H.177 Ligands: 2D8.2, LY0.3 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.116, A:D.123, A:D.123, A:H.177 ZN.7: 5 residues within 4Å: Chain B: H.116, D.123, H.177 Ligands: LY0.8, 2D8.9 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.116, B:D.123, B:D.123, B:H.177

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

2D8.2: 17 residues within 4Å: Chain A: R.83, Q.88, L.91, F.107, V.108, A.109, S.114, H.116, D.123, I.135, Y.161, I.171, E.174, W.176, H.177 Ligands: ZN.1, LY0.3 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:L.91, A:A.109, A:I.135, A:Y.161, A:I.171 Hydrogen bonds: A:R.83, A:R.83, A:Q.88, A:A.109, A:E.174, A:W.176 Water bridges: A:S.114, A:E.115 Salt bridges: A:R.83, A:H.116 2D8.9: 16 residues within 4Å: Chain B: R.83, Q.88, L.91, F.107, A.109, S.114, H.116, D.123, L.134, I.135, Y.161, E.174, W.176, H.177 Ligands: ZN.7, LY0.8 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:L.91, B:A.109, B:Y.161 Hydrogen bonds: B:R.83, B:R.83, B:Q.88, B:A.109, B:S.114, B:W.176 Salt bridges: B:R.83, B:H.116, B:H.177

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

LY0.3: 17 residues within 4Å: Chain A: R.83, Q.88, L.91, F.107, V.108, A.109, S.114, H.116, D.123, I.135, Y.161, I.171, E.174, W.176, H.177 Ligands: ZN.1, 2D8.2 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:L.91, A:A.109, A:I.135, A:Y.161, A:I.171 Hydrogen bonds: A:R.83, A:R.83, A:Q.88, A:A.109, A:E.115, A:E.174 Salt bridges: A:R.83, A:H.116 LY0.8: 16 residues within 4Å: Chain B: R.83, Q.88, L.91, F.107, V.108, A.109, S.114, H.116, D.123, I.135, Y.161, E.174, W.176, H.177 Ligands: ZN.7, 2D8.9 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:L.91, B:A.109, B:Y.161 Hydrogen bonds: B:R.83, B:R.83, B:Q.88, B:A.109, B:W.176 Water bridges: B:E.115 Salt bridges: B:R.83, B:H.116, B:H.177

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

SO4.4: 3 residues within 4Å: Chain A: K.86, R.89, R.90 4 PLIP interactions: 4 interactions with chain A Water bridges: A:R.90, A:R.90 Salt bridges: A:R.89, A:R.90

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 6 residues within 4Å: Chain A: L.27, N.29, N.31, H.32, E.197, D.201 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:N.29, A:N.29, A:N.31, A:H.32, A:E.197 Water bridges: A:E.197, A:D.201

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.6: 3 residues within 4Å: Chain A: R.90 Chain B: H.42, L.43 Ligand excluded by PLIP

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: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

D,D-dipeptidase/D,D-carboxypeptidase

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