SMTL ID : 5a57.1

The structure of GH101 from Streptococcus pneumoniae TIGR4 in complex with PUGT

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.46 Å

Oligo State

monomer

Ligands

3 x CA: CALCIUM ION(Non-covalent)

CA.1: 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.22 CA.2: 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.30, H2O.35, H2O.35 CA.3: 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.68

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

CIT.4: 5 residues within 4Å: Chain A: S.812, N.813, G.885, D.886, E.887 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:D.886 Hydrogen bonds: A:N.813, A:N.813, A:D.886, A:E.887 Water bridges: A:K.833 CIT.5: 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:R.848, A:V.937

1 x 5G0: (Z)-[(3R,4R,5R,6R)-3-acetamido-6-(hydroxymethyl)-4,5-bis(oxidanyl)oxan-2-ylidene]amino] N-phenylcarbamate(Non-covalent)

5G0.6: 13 residues within 4Å: Chain A: H.342, D.343, E.384, W.409, D.449, V.450, N.453, E.481, W.482, W.495, W.552, Q.553 Ligands: GAL.30 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:W.495 Hydrogen bonds: A:D.343, A:E.384, A:N.453, A:E.481, A:Q.553 Water bridges: A:Y.447, A:D.449, A:D.449, A:D.449, A:Q.455, A:E.481

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

EDO.7: 5 residues within 4Å: Chain A: K.320, F.549, Y.558, N.775 Ligands: EDO.19 Ligand excluded by PLIP EDO.8: 3 residues within 4Å: Chain A: V.23, D.101, N.102 Ligand excluded by PLIP EDO.9: 6 residues within 4Å: Chain A: N.322, L.323, D.326, G.327, K.701, P.734 Ligand excluded by PLIP EDO.10: 4 residues within 4Å: Chain A: S.21, V.99, V.100, D.101 Ligand excluded by PLIP EDO.11: 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.12: 4 residues within 4Å: Chain A: Y.248, K.469, E.470, K.473 Ligand excluded by PLIP EDO.13: 6 residues within 4Å: Chain A: Q.553, G.554, R.555, R.848, N.850 Ligands: EDO.14 Ligand excluded by PLIP EDO.14: 5 residues within 4Å: Chain A: D.548, R.555, S.556, D.557 Ligands: EDO.13 Ligand excluded by PLIP EDO.15: 5 residues within 4Å: Chain A: T.67, Y.68, K.69, E.77, L.79 Ligand excluded by PLIP EDO.16: 5 residues within 4Å: Chain A: K.292, H.520, Q.576, H.577, F.578 Ligand excluded by PLIP EDO.17: 4 residues within 4Å: Chain A: Q.147, T.148, D.190, K.191 Ligand excluded by PLIP EDO.18: 2 residues within 4Å: Chain A: K.765, Q.781 Ligand excluded by PLIP EDO.19: 8 residues within 4Å: Chain A: K.320, Y.558, N.559, D.698, K.770, A.774, D.776 Ligands: EDO.7 Ligand excluded by PLIP EDO.20: 2 residues within 4Å: Chain A: W.409, N.410 Ligand excluded by PLIP EDO.21: 3 residues within 4Å: Chain A: V.359, E.360, K.363 Ligand excluded by PLIP EDO.22: 4 residues within 4Å: Chain A: N.59, H.60, R.61, H.87 Ligand excluded by PLIP EDO.23: 6 residues within 4Å: Chain A: H.324, N.559, T.563, L.696, Q.722, P.723 Ligand excluded by PLIP EDO.24: 6 residues within 4Å: Chain A: F.106, F.135, N.138, L.140, H.230, S.231 Ligand excluded by PLIP EDO.25: 4 residues within 4Å: Chain A: G.452, N.453, W.482, H.484 Ligand excluded by PLIP EDO.26: 5 residues within 4Å: Chain A: N.102, Q.103, V.258, A.277, S.280 Ligand excluded by PLIP EDO.27: 7 residues within 4Å: Chain A: Y.538, A.567, Q.643, G.645, S.646, Y.648, T.673 Ligand excluded by PLIP EDO.28: 6 residues within 4Å: Chain A: Y.694, K.701, T.702, Q.731, T.732, N.733 Ligand excluded by PLIP EDO.29: 8 residues within 4Å: Chain A: Y.864, F.866, M.903, N.921, V.922, A.923, Q.924, F.927 Ligand excluded by PLIP

1 x GAL: beta-D-galactopyranose(Non-covalent)

GAL.30: 10 residues within 4Å: Chain A: M.301, F.303, H.342, D.343, W.409, W.411, W.552, Q.553, D.939 Ligands: 5G0.6 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Q.553, A:D.939 Water bridges: A:K.841, A:K.841, A:K.841, A:K.841

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