SMTL ID : 1k9f.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

homo-dimer

Ligands

2 x XYP- XYP- GCV: 4-O-methyl-alpha-D-glucopyranuronic acid-(1-2)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose

XYP-XYP-GCV.1: 20 residues within 4Å: Chain A: W.150, E.158, R.159, N.199, V.200, N.201, K.281, R.318, F.320, Y.322, R.335, K.359, D.364, E.392, Y.393, W.520, G.525, H.527, Y.535, W.540 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.158, A:R.159, A:R.159, A:N.201, A:K.359, A:Y.393, A:Y.393, A:Y.322, A:R.335, A:R.335 Water bridges: A:Q.388, A:G.525 Salt bridges: A:K.281, A:R.318, A:K.359 XYP-XYP-GCV.14: 20 residues within 4Å: Chain B: W.150, E.158, R.159, N.199, V.200, N.201, K.281, R.318, F.320, Y.322, R.335, K.359, D.364, E.392, Y.393, W.520, G.525, H.527, Y.535, W.540 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.159, B:R.159, B:N.201, B:K.359, B:Y.393, B:H.527, B:R.335, B:R.335 Water bridges: B:Q.388, B:G.525 Salt bridges: B:K.281, B:R.318, B:K.359

24 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: R.368, E.369, V.371, E.409, F.413, E.584, L.585 Ligand excluded by PLIP GOL.4: 3 residues within 4Å: Chain A: K.620, K.653, R.656 Ligand excluded by PLIP GOL.5: 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.6: 7 residues within 4Å: Chain A: K.408, D.412, K.425, P.472, D.473, L.474, S.475 Ligand excluded by PLIP GOL.7: 7 residues within 4Å: Chain A: D.547, R.548, D.549 Chain B: Y.664, R.665, G.668, R.679 Ligand excluded by PLIP GOL.8: 7 residues within 4Å: Chain A: R.507, E.510, N.511, L.516, D.583, E.584, H.607 Ligand excluded by PLIP GOL.9: 5 residues within 4Å: Chain A: Q.43, E.53, P.54, Q.55, V.56 Ligand excluded by PLIP GOL.10: 5 residues within 4Å: Chain A: Y.5, E.6, P.7, R.11, R.637 Ligand excluded by PLIP GOL.11: 4 residues within 4Å: Chain A: H.120, R.123, R.467, E.482 Ligand excluded by PLIP GOL.12: 9 residues within 4Å: Chain A: C.319, F.320, A.339, Q.357, I.358, K.359, G.361, P.362, M.363 Ligand excluded by PLIP GOL.13: 3 residues within 4Å: Chain A: D.634, E.635, K.636 Ligand excluded by PLIP GOL.15: 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.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: 3 residues within 4Å: Chain B: K.620, K.653, R.656 Ligand excluded by PLIP GOL.18: 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.19: 7 residues within 4Å: Chain B: K.408, D.412, K.425, P.472, D.473, L.474, S.475 Ligand excluded by PLIP GOL.20: 7 residues within 4Å: Chain A: Y.664, R.665, G.668, R.679 Chain B: D.547, R.548, D.549 Ligand excluded by PLIP GOL.21: 7 residues within 4Å: Chain B: R.507, E.510, N.511, L.516, D.583, E.584, H.607 Ligand excluded by PLIP GOL.22: 5 residues within 4Å: Chain B: Q.43, E.53, P.54, Q.55, V.56 Ligand excluded by PLIP GOL.23: 5 residues within 4Å: Chain B: Y.5, E.6, P.7, R.11, R.637 Ligand excluded by PLIP GOL.24: 4 residues within 4Å: Chain B: H.120, R.123, R.467, E.482 Ligand excluded by PLIP GOL.25: 9 residues within 4Å: Chain B: C.319, F.320, A.339, Q.357, I.358, K.359, G.361, P.362, M.363 Ligand excluded by PLIP GOL.26: 3 residues within 4Å: Chain B: D.634, E.635, K.636 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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