SMTL ID : 4a4a.1

CpGH89 (E483Q, E601Q), from Clostridium perfringens, in complex with its substrate GlcNAc-alpha-1,4-galactose

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

monomer

Ligands

1 x GAL- NDG: 2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-beta-D-galactopyranose(Non-covalent)

GAL-NDG.1: 18 residues within 4Å: Chain A: N.297, C.299, Y.303, W.364, M.367, W.431, H.480, Q.481, W.515, Q.516, L.538, F.564, Q.599, Q.662, W.683, W.809, L.820, Y.823 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:W.431, A:Q.481, A:Q.516, A:Q.516, A:Q.516, A:Q.662, A:Q.662, A:Y.823, A:N.297, A:Y.303, A:W.364, A:Q.481, A:Q.599, A:Y.823 Hydrophobic interactions: A:L.820, A:Y.823 Water bridges: A:H.480, A:Q.481

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

SO4.2: 3 residues within 4Å: Chain A: T.617, R.618, D.619 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:R.618, A:D.619 Water bridges: A:D.287, A:D.287, A:D.287, A:R.618, A:D.619, A:D.619 Salt bridges: A:R.618 SO4.3: 2 residues within 4Å: Chain A: G.674, F.675 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:F.675 SO4.4: 3 residues within 4Å: Chain A: N.224, P.289, R.618 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.224, A:N.224 Salt bridges: A:R.618 SO4.5: 3 residues within 4Å: Chain A: G.24, S.76, K.77 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.24, A:G.24, A:S.76 Salt bridges: A:K.77 SO4.6: 5 residues within 4Å: Chain A: N.38, T.39, E.40, G.41, T.43 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.38, A:G.41, A:N.42 SO4.7: 2 residues within 4Å: Chain A: N.108, N.109 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.109 Water bridges: A:N.109, A:N.109 SO4.8: 4 residues within 4Å: Chain A: R.203, V.204, I.205, G.206 No protein-ligand interaction detected (PLIP) SO4.9: 3 residues within 4Å: Chain A: E.275, T.276, M.277 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.276, A:M.277, A:M.277 Salt bridges: A:K.212 SO4.10: 3 residues within 4Å: Chain A: N.547, R.548, E.551 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.547 Water bridges: A:R.548, A:R.548 SO4.11: 3 residues within 4Å: Chain A: M.119, H.120, T.121 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.121, A:T.121 Salt bridges: A:H.120 SO4.12: 4 residues within 4Å: Chain A: K.103, Y.106, D.875, T.876 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.875, A:D.875

1 x CA: CALCIUM ION(Non-covalent)

CA.13: 6 residues within 4Å: Chain A: L.46, D.49, D.51, T.54, A.146, E.147 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:L.46, A:D.49, A:D.51, A:T.54, A:E.147

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.14: 3 residues within 4Å: Chain A: P.174, W.175, E.178 2 PLIP interactions: 2 interactions with chain A Water bridges: A:P.174, A:E.178 GOL.15: 6 residues within 4Å: Chain A: D.231, S.232, G.233, D.234, G.235, K.236 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.232, A:S.232, A:G.233, A:G.235, A:K.236 Water bridges: A:S.279 GOL.16: 4 residues within 4Å: Chain A: P.544, D.545, W.546, N.547 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:P.544, A:W.546, A:N.547 Water bridges: A:P.544

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ficko-Blean, E. et al., Structural analysis of a bacterial exo-alpha-D-N-acetylglucosaminidase in complex with an unusual disaccharide found in class III mucin. Glycobiology (2012)

Release Date

2012-04-04

Peptides

ALPHA-N-ACETYLGLUCOSAMINIDASE FAMILY PROTEIN: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

ALPHA-N-ACETYLGLUCOSAMINIDASE FAMILY PROTEIN