SMTL ID : 1l8n.1

The 1.5A crystal structure of alpha-D-glucuronidase from Bacillus stearothermophilus T-1, complexed with 4-O-methyl-glucuronic acid and xylotriose

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

homo-dimer

Ligands

2 x XYP- XYP: beta-D-xylopyranose-(1-4)-beta-D-xylopyranose(Non-covalent)

XYP-XYP.1: 14 residues within 4Å: Chain A: R.159, E.285, F.320, Y.322, R.335, D.364, Y.393, W.520, G.525, H.527, Y.535, W.540 Ligands: GCW.2, GOL.16 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:E.285, A:Y.322, A:R.335, A:R.335, A:D.364 Water bridges: A:R.159 XYP-XYP.17: 14 residues within 4Å: Chain B: R.159, E.285, F.320, Y.322, R.335, D.364, Y.393, W.520, G.525, H.527, Y.535, W.540 Ligands: GCW.18, GOL.32 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.285, B:R.335, B:R.335 Water bridges: B:R.159

2 x GCW: 4-O-methyl-beta-D-glucopyranuronic acid(Non-covalent)

GCW.2: 17 residues within 4Å: Chain A: W.150, E.158, R.159, N.199, V.200, N.201, K.281, E.285, R.318, F.320, K.359, D.364, E.392, Y.393, H.527 Ligands: XYP-XYP.1, XYP-XYP.1 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:E.158, A:R.159, A:R.159, A:N.201, A:E.285, A:Y.393, A:Y.393, A:Y.393 Water bridges: A:K.281 Salt bridges: A:K.281, A:R.318, A:K.359, A:K.359 GCW.18: 17 residues within 4Å: Chain B: W.150, E.158, R.159, N.199, V.200, N.201, K.281, E.285, R.318, F.320, K.359, D.364, E.392, Y.393, H.527 Ligands: XYP-XYP.17, XYP-XYP.17 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:R.159, B:R.159, B:N.201, B:E.285, B:Y.393, B:Y.393, B:H.527 Water bridges: B:E.285 Salt bridges: B:K.281, B:R.318, B:K.359, B:K.359

28 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 4 residues within 4Å: Chain A: K.630, Y.638, H.639, L.642 Ligand excluded by PLIP GOL.4: 7 residues within 4Å: Chain A: R.368, E.369, V.371, E.409, F.413, E.584, L.585 Ligand excluded by PLIP GOL.5: 12 residues within 4Å: Chain A: G.519, W.520, M.521, N.531, V.532, D.533, G.534, Y.535, E.536, T.542, Y.543, H.544 Ligand excluded by PLIP GOL.6: 9 residues within 4Å: Chain A: Y.91, Y.116, H.120, R.123, S.189, V.190, G.191, R.467, W.470 Ligand excluded by PLIP GOL.7: 8 residues within 4Å: Chain A: N.451, G.454, H.455, T.456, D.640, V.641, E.643, R.644 Ligand excluded by PLIP GOL.8: 3 residues within 4Å: Chain A: G.674, R.675, K.676 Ligand excluded by PLIP GOL.9: 6 residues within 4Å: Chain A: N.511, E.602, N.610, T.611, E.614, Q.618 Ligand excluded by PLIP GOL.10: 3 residues within 4Å: Chain A: K.620, K.653, R.656 Ligand excluded by PLIP GOL.11: 6 residues within 4Å: Chain A: K.15, S.19, M.50, G.128, E.129, I.131 Ligand excluded by PLIP GOL.12: 6 residues within 4Å: Chain A: W.68, E.75, E.76, F.77, R.94, Y.105 Ligand excluded by PLIP GOL.13: 5 residues within 4Å: Chain A: L.10, R.11, Y.12, K.44, S.48 Ligand excluded by PLIP GOL.14: 6 residues within 4Å: Chain A: T.661, Y.664, R.665, Y.678 Chain B: R.331, D.547 Ligand excluded by PLIP GOL.15: 4 residues within 4Å: Chain A: G.4, R.179, S.448, P.450 Ligand excluded by PLIP GOL.16: 13 residues within 4Å: Chain A: E.285, F.320, Y.322, R.335, D.364, Y.393, W.520, H.527, Y.535, W.540, T.542 Ligands: XYP-XYP.1, XYP-XYP.1 Ligand excluded by PLIP GOL.19: 4 residues within 4Å: Chain B: K.630, Y.638, H.639, L.642 Ligand excluded by PLIP GOL.20: 7 residues within 4Å: Chain B: R.368, E.369, V.371, E.409, F.413, E.584, L.585 Ligand excluded by PLIP GOL.21: 12 residues within 4Å: Chain B: G.519, W.520, M.521, N.531, V.532, D.533, G.534, Y.535, E.536, T.542, Y.543, H.544 Ligand excluded by PLIP GOL.22: 9 residues within 4Å: Chain B: Y.91, Y.116, H.120, R.123, S.189, V.190, G.191, R.467, W.470 Ligand excluded by PLIP GOL.23: 8 residues within 4Å: Chain B: N.451, G.454, H.455, T.456, D.640, V.641, E.643, R.644 Ligand excluded by PLIP GOL.24: 3 residues within 4Å: Chain B: G.674, R.675, K.676 Ligand excluded by PLIP GOL.25: 6 residues within 4Å: Chain B: N.511, E.602, N.610, T.611, E.614, Q.618 Ligand excluded by PLIP GOL.26: 3 residues within 4Å: Chain B: K.620, K.653, R.656 Ligand excluded by PLIP GOL.27: 6 residues within 4Å: Chain B: K.15, S.19, M.50, G.128, E.129, I.131 Ligand excluded by PLIP GOL.28: 6 residues within 4Å: Chain B: W.68, E.75, E.76, F.77, R.94, Y.105 Ligand excluded by PLIP GOL.29: 5 residues within 4Å: Chain B: L.10, R.11, Y.12, K.44, S.48 Ligand excluded by PLIP GOL.30: 6 residues within 4Å: Chain A: R.331, D.547 Chain B: T.661, Y.664, R.665, Y.678 Ligand excluded by PLIP GOL.31: 4 residues within 4Å: Chain B: G.4, R.179, S.448, P.450 Ligand excluded by PLIP GOL.32: 13 residues within 4Å: Chain B: E.285, F.320, Y.322, R.335, D.364, Y.393, W.520, H.527, Y.535, W.540, T.542 Ligands: XYP-XYP.17, XYP-XYP.17 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Golan, G. et al., Crystal Structures of Geobacillus stearothermophilus {alpha}-Glucuronidase Complexed with Its Substrate and Products: MECHANISTIC IMPLICATIONS. J.Biol.Chem. (2004)

Release Date

2003-03-21

Peptides

ALPHA-D-GLUCURONIDASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

ALPHA-D-GLUCURONIDASE

Related Entries With Identical Sequence