SMTL ID : 4f78.1

Crystal Structure of Vancomycin Resistance D,D-dipeptidase VanXYg

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: H.108, D.115, H.168 Ligands: SO4.3 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.108, A:D.115, A:D.115, A:H.168, H2O.1

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

CL.2: 4 residues within 4Å: Chain A: M.3, K.4, T.5, K.228 Ligand excluded by PLIP

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

SO4.3: 10 residues within 4Å: Chain A: R.75, Q.80, Y.99, V.100, A.101, S.106, H.108, D.115, H.168 Ligands: ZN.1 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:Q.80, A:Q.80, A:A.101 Water bridges: A:R.75, A:R.75, A:E.107, A:Y.152, A:E.165, A:E.165 Salt bridges: A:R.75, A:H.108, A:H.168

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

EDO.4: 3 residues within 4Å: Chain A: E.157, E.158 Ligands: EDO.10 No protein-ligand interaction detected (PLIP) EDO.5: 6 residues within 4Å: Chain A: V.36, P.37, A.38, A.52, N.53, Q.56 No protein-ligand interaction detected (PLIP) EDO.6: 4 residues within 4Å: Chain A: F.185, E.189, Q.192, F.193 No protein-ligand interaction detected (PLIP) EDO.7: 4 residues within 4Å: Chain A: L.198, V.218, P.219 Ligands: EDO.8 2 PLIP interactions: 2 interactions with chain A Water bridges: A:E.199, A:Y.217 EDO.8: 4 residues within 4Å: Chain A: L.198, E.199, D.200 Ligands: EDO.7 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.199, A:D.200 EDO.9: 6 residues within 4Å: Chain A: N.22, K.23, N.24, I.159, T.160, G.161 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.23 Water bridges: A:N.24, A:E.158 EDO.10: 6 residues within 4Å: Chain A: K.98, E.157, G.161, I.162, S.163 Ligands: EDO.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.98, A:S.163 EDO.11: 3 residues within 4Å: Chain A: G.92, E.93, D.94 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.93, A:D.94, A:D.94 Water bridges: A:F.95 EDO.12: 4 residues within 4Å: Chain A: E.182, L.204, F.205, E.206 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.182, A:L.204, A:E.206 EDO.13: 3 residues within 4Å: Chain A: D.145, Y.174, R.210 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.210 Water bridges: A:D.145, A:Y.174

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.14: 3 residues within 4Å: Chain A: A.153, R.154, D.155 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.154, A:R.154, A:R.154, A:D.155 GOL.15: 3 residues within 4Å: Chain A: G.65, N.66, S.67 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.66, A:N.66, A:N.66 GOL.16: 8 residues within 4Å: Chain A: Y.14, C.15, G.16, N.17, L.19, V.32, T.110, L.112 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.16, A:T.110 Water bridges: A:N.31

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

2012-05-23

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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