SMTL ID : 5a56.1

The structure of GH101 from Streptococcus pneumoniae TIGR4 in complex with 1-O-methyl-T-antigen

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

monomer

Ligands

1 x MGC- GAL: beta-D-galactopyranose-(1-3)-methyl 2-acetamido-2-deoxy-alpha-D-galactopyranoside(Non-covalent)

MGC-GAL.1: 5 residues within 4Å: Chain A: W.409, W.411, K.841, E.938, D.939 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.841, A:K.841, A:D.939

3 x CA: CALCIUM ION(Non-covalent)

CA.2: 5 residues within 4Å: Chain A: D.262, N.264, D.266, N.268, D.273 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.262, A:D.266, A:N.268, A:D.273, H2O.16 CA.4: 5 residues within 4Å: Chain A: D.918, E.920, E.966, W.969, D.1096 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.918, A:E.920, A:E.966, A:W.969, H2O.52 CA.5: 4 residues within 4Å: Chain A: G.748, N.775, D.776, D.892 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:G.748, A:D.776, A:D.892, H2O.43, H2O.43

1 x MN: MANGANESE (II) ION(Non-covalent)

MN.3: 3 residues within 4Å: Chain A: E.388, D.413, H.943 6 PLIP interactions: 3 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.388, A:D.413, A:H.943, H2O.22, H2O.26, H2O.26

2 x CIT: CITRIC ACID(Non-functional Binders)

CIT.6: 4 residues within 4Å: Chain A: Y.839, T.847, R.848, R.849 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:T.847 Hydrogen bonds: A:R.849 Water bridges: A:Y.839, A:T.847, A:T.847, A:V.937 CIT.7: 5 residues within 4Å: Chain A: S.812, N.813, G.885, D.886, E.887 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:D.886 Hydrogen bonds: A:N.813, A:D.886, A:D.886, A:E.887, A:E.887 Water bridges: A:D.886, A:D.886, A:E.887

31 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.8: 5 residues within 4Å: Chain A: K.916, D.918, N.1097, L.1098, Q.1099 Ligand excluded by PLIP EDO.9: 4 residues within 4Å: Chain A: S.1009, D.1010, N.1076, R.1078 Ligand excluded by PLIP EDO.10: 5 residues within 4Å: Chain A: K.292, H.520, Q.576, H.577, F.578 Ligand excluded by PLIP EDO.11: 3 residues within 4Å: Chain A: V.23, D.101, N.102 Ligand excluded by PLIP EDO.12: 3 residues within 4Å: Chain A: D.167, L.178, K.180 Ligand excluded by PLIP EDO.13: 1 residues within 4Å: Chain A: K.241 Ligand excluded by PLIP EDO.14: 8 residues within 4Å: Chain A: K.320, Y.558, N.559, D.698, K.770, A.774, D.776 Ligands: EDO.27 Ligand excluded by PLIP EDO.15: 6 residues within 4Å: Chain A: H.324, N.559, T.563, L.696, Q.722, P.723 Ligand excluded by PLIP EDO.16: 4 residues within 4Å: Chain A: S.21, V.99, V.100, D.101 Ligand excluded by PLIP EDO.17: 5 residues within 4Å: Chain A: T.67, Y.68, K.69, E.77, L.79 Ligand excluded by PLIP EDO.18: 8 residues within 4Å: Chain A: G.47, Q.48, V.49, Q.50, S.142, E.219, V.221, Y.226 Ligand excluded by PLIP EDO.19: 9 residues within 4Å: Chain A: Y.864, F.866, N.899, M.903, N.921, V.922, A.923, Q.924, F.927 Ligand excluded by PLIP EDO.20: 6 residues within 4Å: Chain A: P.387, D.413, Q.414, D.963, K.972, F.1087 Ligand excluded by PLIP EDO.21: 6 residues within 4Å: Chain A: Y.538, A.567, R.633, Q.643, G.645, Y.648 Ligand excluded by PLIP EDO.22: 5 residues within 4Å: Chain A: N.102, Q.103, V.258, A.277, S.280 Ligand excluded by PLIP EDO.23: 6 residues within 4Å: Chain A: F.106, F.135, N.138, L.140, H.230, S.231 Ligand excluded by PLIP EDO.24: 2 residues within 4Å: Chain A: N.799, T.868 Ligand excluded by PLIP EDO.25: 5 residues within 4Å: Chain A: W.197, K.256, I.281, M.282, N.283 Ligand excluded by PLIP EDO.26: 3 residues within 4Å: Chain A: Q.98, H.105, D.107 Ligand excluded by PLIP EDO.27: 6 residues within 4Å: Chain A: K.320, F.549, Y.558, A.774, N.775 Ligands: EDO.14 Ligand excluded by PLIP EDO.28: 5 residues within 4Å: Chain A: Q.705, L.707, T.715, L.716, D.717 Ligand excluded by PLIP EDO.29: 4 residues within 4Å: Chain A: T.758, T.790, K.792, T.877 Ligand excluded by PLIP EDO.30: 4 residues within 4Å: Chain A: G.206, G.207, D.210, H.484 Ligand excluded by PLIP EDO.31: 8 residues within 4Å: Chain A: Y.574, F.578, D.610, N.614, L.637, P.651, N.653, W.654 Ligand excluded by PLIP EDO.32: 4 residues within 4Å: Chain A: Y.248, K.469, E.470, K.473 Ligand excluded by PLIP EDO.33: 2 residues within 4Å: Chain A: Y.745, H.756 Ligand excluded by PLIP EDO.34: 5 residues within 4Å: Chain A: N.322, D.326, G.327, K.701, P.734 Ligand excluded by PLIP EDO.35: 5 residues within 4Å: Chain A: W.1043, T.1044, D.1045, S.1046, K.1047 Ligand excluded by PLIP EDO.36: 4 residues within 4Å: Chain A: D.644, T.678, T.679, W.680 Ligand excluded by PLIP EDO.37: 2 residues within 4Å: Chain A: N.1073, A.1074 Ligand excluded by PLIP EDO.38: 4 residues within 4Å: Chain A: Q.147, T.148, D.190, K.191 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gregg, K.J. et al., Structural Analysis of a Family 101 Glycoside Hydrolase in Complex with Carbohydrates Reveals Insights into Its Mechanism. J.Biol.Chem. (2015)

Release Date

2015-09-02

Peptides

ENDO-ALPHA-N-ACETYLGALACTOSAMINIDASE: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

ENDO-ALPHA-N-ACETYLGALACTOSAMINIDASE