SMTL ID : 4mur.1

Crystal structure of vancomycin resistance D,D-dipeptidase/D,D-pentapeptidase VanXYc D59S mutant

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

homo-dimer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 3 residues within 4Å: Chain A: H.116, D.123, H.177 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.116, A:D.123, A:H.177, H2O.4, H2O.7 ZN.9: 3 residues within 4Å: Chain B: H.116, D.123, H.177 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.116, B:D.123, B:D.123, B:H.177, H2O.15

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

CL.2: 4 residues within 4Å: Chain A: R.83, Q.88, A.109, S.114 Ligand excluded by PLIP CL.3: 3 residues within 4Å: Chain A: K.86, R.90 Chain B: L.43 Ligand excluded by PLIP CL.4: 3 residues within 4Å: Chain A: N.29, N.31, H.32 Ligand excluded by PLIP CL.11: 5 residues within 4Å: Chain B: R.83, Q.88, V.108, A.109, S.114 Ligand excluded by PLIP CL.12: 3 residues within 4Å: Chain A: H.42, L.43 Chain B: R.90 Ligand excluded by PLIP CL.13: 3 residues within 4Å: Chain A: Y.82 Chain B: T.84, K.86 Ligand excluded by PLIP

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

PE3.5: 2 residues within 4Å: Chain A: H.200, A.204 No protein-ligand interaction detected (PLIP) PE3.6: 5 residues within 4Å: Chain A: M.22, N.23, Q.26, K.35, Q.38 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Q.26 Hydrogen bonds: A:M.22, A:K.35, A:Q.38 PE3.7: 4 residues within 4Å: Chain A: E.58, Q.62, R.65, Y.180 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.65, A:Y.180 PE3.8: 1 residues within 4Å: Chain A: F.210 No protein-ligand interaction detected (PLIP)

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

SO4.10: 3 residues within 4Å: Chain B: K.86, R.89, R.90 4 PLIP interactions: 4 interactions with chain B Water bridges: B:R.89, B:R.89 Salt bridges: B:R.89, B:R.90

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

2013-10-02

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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