SMTL ID : 5fre.1 (2 other biounits)

Characterization of a novel CBM from Clostridium perfringens

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

monomer

Ligands

1 x GAL- SIA: N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose(Non-covalent)

GAL-SIA.1: 9 residues within 4Å: Chain A: I.51, N.64, Y.66, Y.70, E.79, R.81, R.158, N.163, Y.165 12 PLIP interactions: 12 interactions with chain A Water bridges: A:K.63, A:K.63, A:N.64, A:N.64, A:R.81, A:N.64, A:R.158, A:R.158, A:N.163 Hydrophobic interactions: A:I.51, A:Y.70, A:E.79 Hydrogen bonds: A:E.79, A:N.163, A:Y.165 Salt bridges: A:R.81, A:R.158

3 x CA: CALCIUM ION(Non-covalent)

CA.2: 3 residues within 4Å: Chain A: N.45, S.46, D.107 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:S.46, A:D.107, H2O.2, H2O.3, H2O.3 CA.3: 2 residues within 4Å: Chain A: D.136, N.138 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.136, A:D.136, A:N.138, H2O.5, H2O.5 CA.4: 3 residues within 4Å: Chain A: N.157, R.158, E.164 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:R.158, H2O.3, H2O.6, H2O.6, H2O.7

1 x 1PG: 2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL(Non-covalent)

1PG.5: 6 residues within 4Å: Chain A: W.3, E.4, L.5, L.6, Y.185, S.188 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.6

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ribeiro, J.P. et al., Characterization of a High-Affinity Sialic Acid-Specific Cbm40 from Clostridium Perfringens and Engineering of a Divalent Form. Biochem.J. (2016)

Release Date

2016-07-20

Peptides

EXO-ALPHA-SIALIDASE: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

EXO-ALPHA-SIALIDASE

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