SMTL ID : 6dru.1 (1 other biounit)

Xylosidase from Aspergillus niger

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

homo-tetramer

Ligands

2 x NAG- NAG- BMA- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN-MAN.1: 14 residues within 4Å: Chain A: E.260, N.261, E.264, L.267, Y.563, F.564, Q.565, D.566, A.567 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.2, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.2, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.2, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.2, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.2 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.267 NAG-NAG-BMA-MAN-MAN-MAN.23: 14 residues within 4Å: Chain C: E.260, N.261, E.264, L.267, Y.563, F.564, Q.565, D.566, A.567 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.24, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.24, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.24, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.24, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.24 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.267

2 x NAG- NAG- BMA- MAN- MAN- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.2: 14 residues within 4Å: Chain A: E.260, N.261, Q.287, W.289, A.290, D.298, R.300, L.301, P.303, N.358, Y.568 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.1, NAG-NAG-BMA-MAN-MAN-MAN.1, NAG-NAG-BMA-MAN-MAN-MAN.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.260, A:E.260, A:D.298, A:R.300 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.24: 14 residues within 4Å: Chain C: E.260, N.261, Q.287, W.289, A.290, D.298, R.300, L.301, P.303, N.358, Y.568 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.23, NAG-NAG-BMA-MAN-MAN-MAN.23, NAG-NAG-BMA-MAN-MAN-MAN.23 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:E.260, C:D.298, C:D.298, C:R.300, C:Y.568

4 x NAG- NAG- BMA- MAN- MAN- MAN- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.3: 21 residues within 4Å: Chain A: H.158, D.493, A.496, D.523, T.525, N.637, Q.641, T.655, L.656, W.662 Chain B: R.84, Y.100, E.108, L.110, N.113, E.114, Y.115, A.116, P.117, S.142 Ligands: BGC-BGC-BGC-XYS.5 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.113, B:E.114, B:A.116 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.7: 19 residues within 4Å: Chain A: R.84, Y.100, E.108, L.110, N.113, E.114, Y.115, A.116, S.142 Chain B: H.158, D.493, A.496, D.523, T.525, N.637, Q.641, T.655, L.656, W.662 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.114, A:A.116 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.25: 21 residues within 4Å: Chain C: H.158, D.493, A.496, D.523, T.525, N.637, Q.641, T.655, L.656, W.662 Chain D: R.84, Y.100, E.108, L.110, N.113, E.114, Y.115, A.116, P.117, S.142 Ligands: BGC-BGC-BGC-XYS.27 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:N.113, D:E.114, D:A.116 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.29: 19 residues within 4Å: Chain C: R.84, Y.100, E.108, L.110, N.113, E.114, Y.115, A.116, S.142 Chain D: H.158, D.493, A.496, D.523, T.525, N.637, Q.641, T.655, L.656, W.662 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:E.114, C:A.116

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

BGC-BGC-XYS-GAL-BGC.4: 16 residues within 4Å: Chain A: L.257, Y.286, W.357, Q.396, E.404, Y.406, N.409, G.410, Q.411, E.416, F.520, E.521, V.522, S.524, S.559 Ligands: XYS.12 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.286, A:Q.396, A:E.404, A:Y.406, A:Y.406, A:N.409, A:N.409, A:E.416 BGC-BGC-XYS-GAL-BGC.8: 16 residues within 4Å: Chain B: L.257, Y.286, W.325, W.357, Q.396, E.404, Y.406, N.409, G.410, Q.411, E.416, F.520, E.521, S.524, S.559 Ligands: XYS.19 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.286, B:Q.396, B:E.404, B:Y.406, B:Y.406, B:N.409, B:N.409, B:G.410 BGC-BGC-XYS-GAL-BGC.26: 16 residues within 4Å: Chain C: L.257, Y.286, W.357, Q.396, E.404, Y.406, N.409, G.410, Q.411, E.416, F.520, E.521, V.522, S.524, S.559 Ligands: XYS.34 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Y.286, C:Y.286, C:Q.396, C:Y.406, C:Y.406, C:Y.406, C:N.409, C:N.409, C:E.416 BGC-BGC-XYS-GAL-BGC.30: 16 residues within 4Å: Chain D: L.257, Y.286, W.325, W.357, Q.396, E.404, Y.406, N.409, G.410, Q.411, E.416, F.520, E.521, S.524, S.559 Ligands: XYS.41 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:Y.286, D:Y.286, D:Q.396, D:Y.406, D:Y.406, D:Y.406, D:N.409, D:N.409, D:G.410

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

BGC-BGC-BGC-XYS.5: 4 residues within 4Å: Chain A: W.527, T.534, Y.563 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.3 No protein-ligand interaction detected (PLIP) BGC-BGC-BGC-XYS.27: 4 residues within 4Å: Chain C: W.527, T.534, Y.563 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.25 No protein-ligand interaction detected (PLIP)

2 x NAG- NAG- BMA- MAN- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.6: 13 residues within 4Å: Chain B: E.260, N.261, T.263, Q.287, W.289, A.290, D.298, R.300, L.301, P.303, N.358, Y.568 Ligands: NAG.15 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.260, B:R.300, B:R.300, B:R.300 Water bridges: B:E.260 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.28: 13 residues within 4Å: Chain D: E.260, N.261, T.263, Q.287, W.289, A.290, D.298, R.300, L.301, P.303, N.358, Y.568 Ligands: NAG.37 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:E.260, D:R.300, D:R.300, D:R.300, D:Y.568 Water bridges: D:D.298

18 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.9: 3 residues within 4Å: Chain A: W.681, N.683, R.709 Ligand excluded by PLIP NAG.10: 2 residues within 4Å: Chain A: N.6, T.75 Ligand excluded by PLIP NAG.11: 2 residues within 4Å: Chain A: N.453, D.456 Ligand excluded by PLIP NAG.13: 1 residues within 4Å: Chain A: N.314 Ligand excluded by PLIP NAG.15: 8 residues within 4Å: Chain B: E.260, N.261, T.263, E.264, A.567 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.6, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.6, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.6 Ligand excluded by PLIP NAG.16: 3 residues within 4Å: Chain B: W.681, N.683, R.709 Ligand excluded by PLIP NAG.17: 2 residues within 4Å: Chain B: N.6, T.75 Ligand excluded by PLIP NAG.18: 2 residues within 4Å: Chain B: N.453, D.456 Ligand excluded by PLIP NAG.20: 1 residues within 4Å: Chain B: N.314 Ligand excluded by PLIP NAG.31: 3 residues within 4Å: Chain C: W.681, N.683, R.709 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain C: N.6, T.75 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain C: N.453, D.456 Ligand excluded by PLIP NAG.35: 1 residues within 4Å: Chain C: N.314 Ligand excluded by PLIP NAG.37: 8 residues within 4Å: Chain D: E.260, N.261, T.263, E.264, A.567 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.28, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.28, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.28 Ligand excluded by PLIP NAG.38: 3 residues within 4Å: Chain D: W.681, N.683, R.709 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain D: N.6, T.75 Ligand excluded by PLIP NAG.40: 2 residues within 4Å: Chain D: N.453, D.456 Ligand excluded by PLIP NAG.42: 1 residues within 4Å: Chain D: N.314 Ligand excluded by PLIP

4 x XYS: alpha-D-xylopyranose(Non-covalent)

XYS.12: 12 residues within 4Å: Chain A: L.257, D.285, Y.286, W.325, W.393, D.395, R.470, W.484, D.487, F.520, H.557 Ligands: BGC-BGC-XYS-GAL-BGC.4 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:D.395, A:R.470, A:D.487, A:H.557 Water bridges: A:Y.286, A:W.484, A:D.516 XYS.19: 13 residues within 4Å: Chain B: L.257, D.285, Y.286, W.325, W.393, D.395, Q.396, R.470, W.484, D.487, F.520, H.557 Ligands: BGC-BGC-XYS-GAL-BGC.8 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:D.395, B:R.470, B:D.487, B:D.487, B:H.557 XYS.34: 12 residues within 4Å: Chain C: L.257, D.285, Y.286, W.325, W.393, D.395, R.470, W.484, D.487, F.520, H.557 Ligands: BGC-BGC-XYS-GAL-BGC.26 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:D.395, C:R.470, C:D.487, C:H.557 Water bridges: C:Y.286, C:D.487, C:D.487 XYS.41: 13 residues within 4Å: Chain D: L.257, D.285, Y.286, W.325, W.393, D.395, Q.396, R.470, W.484, D.487, F.520, H.557 Ligands: BGC-BGC-XYS-GAL-BGC.30 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:D.395, D:R.470, D:D.487, D:D.487, D:H.557 Water bridges: D:D.487, D:D.487

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.14: 4 residues within 4Å: Chain A: T.368, R.373, W.441, Q.445 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.368, A:R.373, A:R.373, A:Q.445 GOL.21: 4 residues within 4Å: Chain B: T.68, T.69, T.71, E.72 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:T.68, B:T.69, B:E.72 Water bridges: B:T.68, B:E.72 GOL.22: 5 residues within 4Å: Chain B: I.44, T.368, R.373, W.441, Q.445 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.373, B:R.373, B:Q.445 GOL.36: 4 residues within 4Å: Chain C: T.368, R.373, W.441, Q.445 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:T.368, C:R.373, C:R.373, C:Q.445 GOL.43: 4 residues within 4Å: Chain D: T.68, T.69, T.71, E.72 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:T.68, D:T.69, D:E.72 Water bridges: D:T.68, D:E.72 GOL.44: 5 residues within 4Å: Chain D: I.44, T.368, R.373, W.441, Q.445 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:R.373, D:R.373, D:Q.445

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cao, H. et al., Crystal Structure of alpha-Xylosidase fromAspergillus nigerin Complex with a Hydrolyzed Xyloglucan Product and New Insights in Accurately Predicting Substrate Specificities of GH31 Family Glycosidases. Acs Sustain Chem Eng (2020)

Release Date

2018-08-22

Peptides

Glycosyl hydrolases family 31 family protein: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Glycosyl hydrolases family 31 family protein

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