SMTL ID : 4knl.3 (3 other biounits)

Crystal structure of Staphylococcus aureus hydrolase AmiA in complex with its ligand

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

monomer

Ligands

1 x ALA- ZGL- ALY- DAL- NH2: Muramyl tetrapeptide(Non-covalent)

ALA-ZGL-ALY-DAL-NH2.1: 15 residues within 4Å: Chain A: Q.90, N.91, A.92, W.114, G.115, V.116, G.117, A.118, N.121, E.128, H.174, T.184, H.186 Ligands: MPD.4, MUB.7 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:W.114, A:W.114, A:W.114 Hydrogen bonds: A:N.91, A:G.115, A:V.116, A:G.117, A:N.121, A:E.128, A:T.184, A:T.184 Water bridges: A:N.91, A:D.185

1 x IMD: IMIDAZOLE(Non-covalent)

IMD.2: 5 residues within 4Å: Chain A: P.23, N.30, D.31, C.34, E.209 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.209 Water bridges: A:N.30

2 x NA: SODIUM ION(Non-functional Binders)

NA.3: 4 residues within 4Å: Chain A: D.161, S.162, D.166, N.168 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.168 Water bridges: A:D.166 NA.6: 3 residues within 4Å: Chain A: T.109, Q.152, Y.156 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.109, A:Y.156

1 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.4: 4 residues within 4Å: Chain A: Y.54, L.112, W.114 Ligands: ALA-ZGL-ALY-DAL-NH2.1 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Y.54, A:Y.54, A:L.112, A:W.114

1 x TAR: D(-)-TARTARIC ACID(Non-covalent)

TAR.5: 4 residues within 4Å: Chain A: Y.47, T.48, S.49, K.86 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Y.47, A:Y.47, A:S.49 Water bridges: A:Y.47, A:K.86 Salt bridges: A:K.86

1 x MUB: N-acetyl-alpha-muramic acid(Non-covalent)

MUB.7: 7 residues within 4Å: Chain A: T.71, N.73, E.81, F.97, E.128, H.186 Ligands: ALA-ZGL-ALY-DAL-NH2.1 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.97, A:E.128 Hydrogen bonds: A:T.71, A:N.73, A:E.81, A:H.186

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Buttner, F.M. et al., Structure-function analysis of Staphylococcus aureus amidase reveals the determinants of peptidoglycan recognition and cleavage. J.Biol.Chem. (2014)

Release Date

2014-03-12

Peptides

Bifunctional autolysin: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

Bifunctional autolysin

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