SMTL ID : 1k9e.1

Crystal structure of a mutated family-67 alpha-D-glucuronidase (E285N) from Bacillus stearothermophilus T-6, complexed with 4-O-methyl-glucuronic acid

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-dimer

Ligands

2 x GCV: 4-O-methyl-alpha-D-glucopyranuronic acid(Non-covalent)

GCV.1: 15 residues within 4Å: Chain A: W.150, E.158, R.159, N.199, V.200, N.201, K.281, R.318, F.320, K.359, D.364, E.392, Y.393, H.527 Ligands: GOL.5 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:E.158, A:R.159, A:R.159, A:N.201, A:Y.393, A:Y.393 Water bridges: A:K.281 Salt bridges: A:K.281, A:K.281, A:R.318, A:K.359, A:K.359 GCV.13: 15 residues within 4Å: Chain B: W.150, E.158, R.159, N.199, V.200, N.201, K.281, R.318, F.320, K.359, D.364, E.392, Y.393, H.527 Ligands: GOL.17 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:R.159, B:R.159, B:N.201, B:Y.393, B:H.527 Water bridges: B:K.281 Salt bridges: B:K.281, B:K.281, B:R.318, B:K.359, B:K.359

22 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 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.3: 7 residues within 4Å: Chain A: W.68, D.74, E.75, E.76, F.77, R.94, Y.105 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: 11 residues within 4Å: Chain A: F.320, Y.322, R.335, D.364, Y.393, W.520, H.527, Y.535, W.540, T.542 Ligands: GCV.1 Ligand excluded by PLIP GOL.6: 7 residues within 4Å: Chain A: A.309, G.312, G.313, E.352, N.353, R.436, Y.437 Ligand excluded by PLIP GOL.7: 10 residues within 4Å: Chain A: Q.326, T.333, D.334, R.335, G.541, T.542, Y.543, Y.545, V.553, R.555 Ligand excluded by PLIP GOL.8: 3 residues within 4Å: Chain A: G.674, R.675, K.676 Ligand excluded by PLIP GOL.9: 7 residues within 4Å: Chain A: S.19, L.21, M.50, L.125, G.128, E.129, I.131 Ligand excluded by PLIP GOL.10: 8 residues within 4Å: Chain A: Y.340, K.344, A.377, A.565, Q.566, Y.567, F.568, P.569 Ligand excluded by PLIP GOL.11: 7 residues within 4Å: Chain A: T.332, T.333, D.334, R.335, K.337, A.338, D.341 Ligand excluded by PLIP GOL.12: 2 residues within 4Å: Chain A: L.81, S.135 Ligand excluded by PLIP GOL.14: 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.15: 7 residues within 4Å: Chain B: W.68, D.74, E.75, E.76, F.77, R.94, Y.105 Ligand excluded by PLIP GOL.16: 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.17: 11 residues within 4Å: Chain B: F.320, Y.322, R.335, D.364, Y.393, W.520, H.527, Y.535, W.540, T.542 Ligands: GCV.13 Ligand excluded by PLIP GOL.18: 7 residues within 4Å: Chain B: A.309, G.312, G.313, E.352, N.353, R.436, Y.437 Ligand excluded by PLIP GOL.19: 10 residues within 4Å: Chain B: Q.326, T.333, D.334, R.335, G.541, T.542, Y.543, Y.545, V.553, R.555 Ligand excluded by PLIP GOL.20: 3 residues within 4Å: Chain B: G.674, R.675, K.676 Ligand excluded by PLIP GOL.21: 7 residues within 4Å: Chain B: S.19, L.21, M.50, L.125, G.128, E.129, I.131 Ligand excluded by PLIP GOL.22: 8 residues within 4Å: Chain B: Y.340, K.344, A.377, A.565, Q.566, Y.567, F.568, P.569 Ligand excluded by PLIP GOL.23: 7 residues within 4Å: Chain B: T.332, T.333, D.334, R.335, K.337, A.338, D.341 Ligand excluded by PLIP GOL.24: 2 residues within 4Å: Chain B: L.81, S.135 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

2002-10-29

Peptides

alpha-D-glucuronidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

alpha-D-glucuronidase

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