SMTL ID : 4oak.1

Crystal structure of vancomycin resistance D,D-dipeptidase/D,D-pentapeptidase VanXYc D59S mutant in complex with D-Alanine-D-Alanine and copper (II)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

2 x CU: COPPER (II) ION(Non-covalent)

CU.1: 5 residues within 4Å: Chain A: H.116, D.123, H.177 Ligands: DAL.2, DAL.3 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:H.116, A:D.123, A:D.123, A:H.177, DAL.2 CU.12: 4 residues within 4Å: Chain B: H.116, D.123, H.177 Ligands: DAL.13 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Ligand interactions Metal complexes: B:H.116, B:D.123, B:D.123, B:H.177, DAL.13

4 x DAL: D-ALANINE(Non-covalent)

DAL.2: 10 residues within 4Å: Chain A: R.83, F.107, H.116, D.123, L.134, E.174, W.176, H.177 Ligands: CU.1, DAL.3 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.134 Hydrogen bonds: A:R.83, A:E.174 DAL.3: 12 residues within 4Å: Chain A: R.83, Q.88, F.107, V.108, A.109, S.114, H.116, Y.161, I.171, E.174 Ligands: CU.1, DAL.2 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:A.109, A:I.171 Hydrogen bonds: A:Q.88, A:F.107, A:A.109 Salt bridges: A:R.83, A:H.116 DAL.13: 11 residues within 4Å: Chain B: R.83, L.91, F.107, H.116, D.123, I.135, E.174, W.176, H.177 Ligands: CU.12, DAL.14 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:L.91, B:I.135 Hydrogen bonds: B:R.83, B:W.176 DAL.14: 9 residues within 4Å: Chain B: R.83, Q.88, F.107, A.109, S.114, H.116, Y.161, E.174 Ligands: DAL.13 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:A.109, B:Y.161 Hydrogen bonds: B:Q.88, B:F.107, B:A.109, B:S.114 Salt bridges: B:R.83, B:H.116, B:H.177

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

SO4.4: 6 residues within 4Å: Chain A: E.163, D.164, K.165, Q.166, S.172, Y.173 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.164, A:K.165, A:Q.166, A:Y.173 SO4.15: 5 residues within 4Å: Chain A: H.42, L.43 Chain B: K.86, R.89, R.90 7 PLIP interactions: 5 interactions with chain B, 2 interactions with chain A Water bridges: B:R.89, B:R.89 Salt bridges: B:K.86, B:R.89, B:R.90, A:H.42 Hydrogen bonds: A:L.43 SO4.16: 4 residues within 4Å: Chain A: T.84 Chain B: T.84, K.86, R.90 4 PLIP interactions: 4 interactions with chain B Water bridges: B:E.85, B:E.87, B:R.90 Salt bridges: B:R.90

1 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 2 residues within 4Å: Chain A: E.87 Chain B: E.87 6 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: B:E.87, A:E.87, H2O.1, H2O.2, H2O.5, H2O.12

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

CL.6: 2 residues within 4Å: Chain A: G.100, L.101 Ligand excluded by PLIP CL.7: 1 residues within 4Å: Chain A: R.90 Ligand excluded by PLIP CL.8: 1 residues within 4Å: Chain A: T.84 Ligand excluded by PLIP CL.9: 2 residues within 4Å: Chain A: N.29, H.32 Ligand excluded by PLIP CL.17: 2 residues within 4Å: Chain B: H.32, E.197 Ligand excluded by PLIP CL.18: 1 residues within 4Å: Chain B: D.164 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)

PE3.10: 1 residues within 4Å: Chain A: F.210 No protein-ligand interaction detected (PLIP) PE3.11: 2 residues within 4Å: Chain A: H.200, A.204 No protein-ligand interaction detected (PLIP) PE3.19: 4 residues within 4Å: Chain B: M.22, P.41, H.42, Q.56 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:M.22, B:H.42, B:Q.56 Water bridges: B:M.22 PE3.20: 5 residues within 4Å: Chain B: W.194, E.198, D.201, Y.202, Q.205 No protein-ligand interaction detected (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

2014-01-15

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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