SMTL ID : 3zmr.1 (1 other biounit)

Bacteroides ovatus GH5 xyloglucanase in complex with a XXXG heptasaccharide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.43 Å

Oligo State

monomer

Ligands

1 x BGC- BGC- BGC- BGC- XYS- XYS- XYS: alpha-D-xylopyranose-(1-6)-beta-D-glucopyranose-(1-4)-[alpha-D-xylopyranose-(1-6)]beta-D-glucopyranose-(1-4)-[alpha-D-xylopyranose-(1-6)]beta-D-glucopyranose-(1-4)-beta-D-glucopyranose(Non-covalent)

BGC-BGC-BGC-BGC-XYS-XYS-XYS.1: 17 residues within 4Å: Chain A: N.130, V.135, I.136, V.137, C.149, W.150, H.216, W.217, N.261, E.262, H.336, Y.338, I.345, E.395, W.437 Ligands: EDO.8, GLC.9 2 PLIP interactions: 2 interactions with chain A Water bridges: A:C.149, A:W.150

1 x BTB: 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-covalent)

BTB.2: 4 residues within 4Å: Chain A: P.105, D.106, N.107, T.108 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.107, A:N.107 Water bridges: A:N.107 Salt bridges: A:D.106

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

EDO.3: 4 residues within 4Å: Chain A: S.354, D.364, L.404, A.408 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.354, A:S.354, A:D.364 EDO.4: 5 residues within 4Å: Chain A: Y.278, A.314, K.315, A.318, H.319 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.314 Water bridges: A:Y.278, A:H.319, A:H.319 EDO.5: 4 residues within 4Å: Chain A: Y.187, W.221, L.233, R.236 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.236 EDO.6: 3 residues within 4Å: Chain A: Y.14, T.27, Y.57 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.14, A:Y.14 EDO.7: 5 residues within 4Å: Chain A: N.310, T.311, D.312, H.336, Y.338 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.312 Water bridges: A:V.313, A:Y.338 EDO.8: 8 residues within 4Å: Chain A: W.150, G.151, N.152, A.439, G.440, Y.441 Ligands: BGC-BGC-BGC-BGC-XYS-XYS-XYS.1, BGC-BGC-BGC-BGC-XYS-XYS-XYS.1 1 PLIP interactions: 1 interactions with chain A Water bridges: A:A.439 EDO.10: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

1 x GLC: alpha-D-glucopyranose(Non-covalent)

GLC.9: 11 residues within 4Å: Chain A: H.216, N.261, E.262, H.336, Y.338, I.345, E.395, W.437 Ligands: BGC-BGC-BGC-BGC-XYS-XYS-XYS.1, BGC-BGC-BGC-BGC-XYS-XYS-XYS.1, BGC-BGC-BGC-BGC-XYS-XYS-XYS.1 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:H.216, A:N.261, A:E.262 Water bridges: A:N.130, A:H.216, A:E.262

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Larsbrink, J. et al., A Discrete Genetic Locus Confers Xyloglucan Metabolism in Select Human Gut Bacteroidetes. Nature (2014)

Release Date

2014-01-15

Peptides

CELLULASE (GLYCOSYL HYDROLASE FAMILY 5): A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

CELLULASE (GLYCOSYL HYDROLASE FAMILY 5)

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