SMTL ID : 6p2o.2 (1 other biounit)

Crystal structure of Streptomyces rapamycinicus GH74 in complex with xyloglucan fragments XLLG and XXXG

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.88 Å

Oligo State

monomer

Ligands

1 x BGC- BGC- BGC- BGC- XYS- XYS- GAL- XYS- GAL: alpha-D-xylopyranose-(1-6)-beta-D-glucopyranose-(1-4)-[beta-D-galactopyranose-(1-2)-alpha-D-xylopyranose-(1-6)]beta-D-glucopyranose-(1-4)-[beta-D-galactopyranose-(1-2)-alpha-D-xylopyranose-(1-6)]beta-D-glucopyranose-(1-4)-beta-D-glucopyranose

BGC-BGC-BGC-BGC-XYS-XYS-GAL-XYS-GAL.1: 19 residues within 4Å: Chain A: G.14, F.15, D.34, I.35, W.60, Y.85, W.89, N.118, R.122, S.178, Y.180, Y.262, A.425, D.444, W.697, N.717 Ligands: BGC-BGC-BGC-BGC-XYS-XYS-XYS.2, BGC-BGC-BGC-BGC-XYS-XYS-XYS.2, GOL.7 5 PLIP interactions: 5 interactions with chain A Water bridges: A:W.89, A:W.89, A:Y.180 Hydrogen bonds: A:S.178, A:S.178, A:N.118, A:R.122, A:Y.262, A:Y.262

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

BGC-BGC-BGC-BGC-XYS-XYS-XYS.2: 14 residues within 4Å: Chain A: F.15, Y.262, W.315, W.316, F.359, E.367, K.371, W.374, M.375, G.394, D.444 Ligands: BGC-BGC-BGC-BGC-XYS-XYS-GAL-XYS-GAL.1, BGC-BGC-BGC-BGC-XYS-XYS-GAL-XYS-GAL.1, BGC-BGC-BGC-BGC-XYS-XYS-GAL-XYS-GAL.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.394, A:G.394

4 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 4 residues within 4Å: Chain A: T.169, Y.170, D.212, K.213 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:K.213 Water bridges: A:T.169, A:T.169, A:T.169, A:T.169, A:T.169, A:V.171, A:V.171 SO4.4: 3 residues within 4Å: Chain A: K.569, R.591, S.633 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.633 Water bridges: A:N.566 Salt bridges: A:K.569, A:R.591 SO4.5: 2 residues within 4Å: Chain A: N.402, N.405 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.402, A:N.405 SO4.6: 3 residues within 4Å: Chain A: R.271, K.280, A.329 5 PLIP interactions: 5 interactions with chain A Water bridges: A:Y.250, A:R.271, A:R.271 Salt bridges: A:R.271, A:K.280

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 4 residues within 4Å: Chain A: S.88, W.89, S.178 Ligands: BGC-BGC-BGC-BGC-XYS-XYS-GAL-XYS-GAL.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.88, A:S.88 Water bridges: A:T.177, A:T.177 GOL.8: 3 residues within 4Å: Chain A: R.134, S.136, T.152 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.134, A:R.134, A:S.136, A:T.152 Water bridges: A:S.154 GOL.9: 3 residues within 4Å: Chain A: S.463, P.464, T.465 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.463, A:T.465 Water bridges: A:G.360, A:G.360, A:T.465, A:T.465

4 x CL: CHLORIDE ION(Non-functional Binders)

CL.10: 1 residues within 4Å: Chain A: D.287 Ligand excluded by PLIP CL.11: 1 residues within 4Å: Chain A: R.346 Ligand excluded by PLIP CL.12: 2 residues within 4Å: Chain A: S.198, S.199 Ligand excluded by PLIP CL.13: 3 residues within 4Å: Chain A: K.6, D.454, R.723 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Arnal, G. et al., Substrate specificity, regiospecificity, and processivity in glycoside hydrolase family 74. J.Biol.Chem. (2019)

Release Date

2019-07-31

Peptides

Xyloglucanase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Xyloglucanase

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