SMTL ID : 3d2z.2 (1 other biounit)

Complex of the N-acetylmuramyl-L-alanine amidase AmiD from E.coli with the product L-Ala-D-gamma-Glu-L-Lys

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-dimer

Ligands

2 x ALA- FGA- LYS: L-Ala-D-gamma-Glu-L-Lys peptide(Non-covalent)

ALA-FGA-LYS.1: 12 residues within 4Å: Chain A: H.35, V.53, W.83, H.84, A.85, G.86, N.97, E.104, H.151, R.158, K.159 Ligands: ZN.2 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:V.53, A:W.83 Hydrogen bonds: A:H.84, A:H.84, A:G.86, A:N.97, A:E.104 Salt bridges: A:H.151, A:R.158, A:K.159 ALA-FGA-LYS.5: 12 residues within 4Å: Chain B: H.35, V.53, W.83, H.84, A.85, G.86, N.97, E.104, H.151, R.158, K.159 Ligands: ZN.6 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:V.53, B:W.83 Hydrogen bonds: B:H.84, B:H.84, B:G.86, B:N.97, B:E.104 Water bridges: B:H.151 Salt bridges: B:H.151, B:R.158, B:K.159

4 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: H.35, H.151, D.161 Ligands: ALA-FGA-LYS.1 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.35, A:H.151, A:D.161, A:D.161, H2O.3 ZN.3: 3 residues within 4Å: Chain B: D.17, R.19, R.20 No protein-ligand interaction detected (PLIP) ZN.6: 4 residues within 4Å: Chain B: H.35, H.151, D.161 Ligands: ALA-FGA-LYS.5 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.35, B:H.151, B:D.161, B:D.161, H2O.6 ZN.7: 3 residues within 4Å: Chain A: D.17, R.19, R.20 No protein-ligand interaction detected (PLIP)

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

CL.4: 1 residues within 4Å: Chain B: R.19 Ligand excluded by PLIP CL.8: 1 residues within 4Å: Chain A: R.19 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kerff, F. et al., Specific Structural Features of the N-Acetylmuramoyl-l-Alanine Amidase AmiD from Escherichia coli and Mechanistic Implications for Enzymes of This Family. J.Mol.Biol. (2010)

Release Date

2009-06-16

Peptides

N-acetylmuramoyl-L-alanine amidase amiD: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

N-acetylmuramoyl-L-alanine amidase amiD

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