SMTL ID : 4uz3.1 (2 other biounits)

Crystal structure of the N-terminal LysM domains from the putative NlpC/P60 D,L endopeptidase from T. thermophilus bound to N-acetyl-chitohexaose

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

monomer

Ligands

1 x NDG- NAG- NAG- NAG- NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose

NDG-NAG-NAG-NAG-NAG-NAG.1: 16 residues within 4Å: Chain A: V.7, A.8, P.9, G.10, D.11, T.12, L.13, Y.14, R.18, F.36, L.37, L.38, Q.39, P.40, R.66 Ligands: DIO.6 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:V.7 Hydrogen bonds: A:G.10, A:L.38, A:Q.39, A:Y.14 Water bridges: A:R.66, A:R.66, A:R.66 Salt bridges: A:R.66

1 x NAG- NAG- NAG- NAG- NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-NAG-NAG-NAG-NAG.2: 5 residues within 4Å: Chain A: E.34, S.35, F.36 Ligands: NDG.3, DIO.6 No protein-ligand interaction detected (PLIP)

1 x NDG: 2-acetamido-2-deoxy-alpha-D-glucopyranose(Non-functional Binders)

NDG.3: 2 residues within 4Å: Ligands: NAG-NAG-NAG-NAG-NAG-NAG.2, NAG-NAG-NAG-NAG-NAG-NAG.2 No protein-ligand interaction detected (PLIP)

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

SO4.4: 2 residues within 4Å: Chain A: T.23, R.67 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.67 Salt bridges: A:R.67 SO4.5: 3 residues within 4Å: Chain A: E.50, R.51, T.52 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.51, A:T.52 Salt bridges: A:R.51

1 x DIO: 1,4-DIETHYLENE DIOXIDE(Non-covalent)

DIO.6: 6 residues within 4Å: Chain A: F.36, L.37 Ligands: NDG-NAG-NAG-NAG-NAG-NAG.1, NDG-NAG-NAG-NAG-NAG-NAG.1, NAG-NAG-NAG-NAG-NAG-NAG.2, NAG-NAG-NAG-NAG-NAG-NAG.2 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wong, J.E.M.M. et al., An Intermolecular Binding Mechanism Involving Multiple Lysm Domains Mediates Carbohydrate Recognition by an Endopeptidase. Acta Crystallogr.,Sect.D (2015)

Release Date

2015-01-14

Peptides

CELL WALL-BINDING ENDOPEPTIDASE-RELATED PROTEIN: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

CELL WALL-BINDING ENDOPEPTIDASE-RELATED PROTEIN

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