SMTL ID : 6en3.1

Crystal structure of full length EndoS from Streptococcus pyogenes in complex with G2 oligosaccharide.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

monomer

Ligands

1 x NAG- BMA- MAN- NAG- GAL- MAN- NAG- GAL: beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-BMA-MAN-NAG-GAL-MAN-NAG-GAL.1: 23 residues within 4Å: Chain A: R.84, W.86, F.115, H.116, D.117, W.118, P.149, R.151, F.152, N.158, A.198, L.200, D.202, S.203, Q.268, Y.270, E.314, E.315, N.316, A.317, N.321, W.323, Y.367 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.367, A:Y.367, A:N.158, A:R.151, A:D.202, A:D.202, A:S.203, A:R.151

1 x CA: CALCIUM ION(Non-covalent)

CA.2: 5 residues within 4Å: Chain A: K.751, D.754, Q.756, P.880, E.881 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:K.751, A:D.754, A:Q.756, A:P.880, H2O.1

1 x NI: NICKEL (II) ION(Non-covalent)

NI.3: 3 residues within 4Å: Chain A: Q.377, F.387, D.392 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:F.387, A:D.392, H2O.1, H2O.1, H2O.1

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Trastoy, B. et al., Structural basis for the recognition of complex-type N-glycans by Endoglycosidase S. Nat Commun (2018)

Release Date

2018-06-13

Peptides

Endo-beta-N-acetylglucosaminidase F2,Multifunctional-autoprocessing repeats-in-toxin: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Endo-beta-N-acetylglucosaminidase F2,Multifunctional-autoprocessing repeats-in-toxin