SMTL ID : 5fqf.2 (1 other biounit)

The details of glycolipid glycan hydrolysis by the structural analysis of a family 123 glycoside hydrolase from Clostridium perfringens

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

monomer

Ligands

2 x NGA: 2-acetamido-2-deoxy-beta-D-galactopyranose(Non-covalent)

NGA.1: 9 residues within 4Å: Chain A: W.203, W.253, Q.256, Y.446, C.448, T.449, W.482, W.500, D.504 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:W.203, A:Y.446 Hydrogen bonds: A:W.253, A:Q.256, A:Q.256, A:Y.446, A:Y.446, A:T.449, A:D.504 Water bridges: A:D.367, A:D.367, A:E.368, A:W.482 NGA.2: 6 residues within 4Å: Chain A: S.194, T.196, N.197, R.242, G.300, F.301 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.301 Hydrogen bonds: A:R.242, A:R.242 Water bridges: A:N.197

7 x FMT: FORMIC ACID(Non-functional Binders)

FMT.3: 4 residues within 4Å: Chain A: G.231, K.518, T.519, F.520 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.519, A:F.520 FMT.4: 2 residues within 4Å: Chain A: R.315, E.326 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.315 FMT.5: 1 residues within 4Å: Chain A: Y.258 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Y.258 FMT.6: 6 residues within 4Å: Chain A: L.353, E.354, G.357, W.358, F.359, N.360 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.354, A:F.359, A:N.360 FMT.7: 3 residues within 4Å: Chain A: W.107, H.132, N.133 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.133, A:N.133 Water bridges: A:N.133, A:N.133 FMT.8: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) FMT.9: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Noach, I. et al., The Details of Glycolipid Glycan Hydrolysis by the Structural Analysis of a Family 123 Glycoside Hydrolase from Clostridium Perfringens. J.Mol.Biol. (2016)

Release Date

2016-03-30

Peptides

BETA-N-ACETYLGALACTOSAMINIDASE: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

BETA-N-ACETYLGALACTOSAMINIDASE

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