SMTL ID : 5ae6.1

The structure of Hypocrea jecorina beta-xylosidase Xyl3A (Bxl1) in complex with 4-thioxylobiose

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

1 x NAG- NAG- BMA- MAN: alpha-D-mannopyranose-(1-3)-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.1: 13 residues within 4Å: Chain A: N.123, T.125, L.126, Q.129, A.382, W.383, N.384, I.385, E.392, R.700, L.701, A.702 Ligands: NAG-NAG-BMA.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.382, A:N.384, A:Q.129, A:Q.129

5 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.2: 2 residues within 4Å: Chain A: W.330, N.333 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:W.330 NAG-NAG.4: 2 residues within 4Å: Chain A: N.420, F.452 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 8 residues within 4Å: Chain B: N.123, T.125, L.126, Q.129, E.392, R.700, L.701, A.702 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.129, B:Q.129 NAG-NAG.7: 3 residues within 4Å: Chain B: W.330, N.333, E.334 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:W.330 NAG-NAG.9: 5 residues within 4Å: Chain B: N.420, L.440, F.452 Ligands: NAG-NAG-BMA-MAN-MAN.8, NAG-NAG-BMA-MAN-MAN.8 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.3: 10 residues within 4Å: Chain A: D.381, A.382, N.384, Y.387, Y.435, I.437, K.445, S.552, V.555 Ligands: NAG-NAG-BMA-MAN.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.441, A:K.445

2 x TXB- XYP: beta-D-xylopyranose-(1-4)-4-deoxy-4-thio-alpha-D-xylopyranose(Non-covalent)

TXB-XYP.5: 16 residues within 4Å: Chain A: Q.14, P.15, L.17, W.87, E.89, Y.152, R.166, K.206, H.207, R.221, M.254, Y.257, D.291, C.292, Y.429, E.492 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:Q.14, A:Y.429, A:Y.429, A:R.166, A:R.166, A:K.206, A:H.207, A:R.221, A:Y.257, A:Y.429 Water bridges: A:P.15, A:K.206 TXB-XYP.10: 16 residues within 4Å: Chain B: Q.14, P.15, L.17, W.87, E.89, Y.152, R.166, K.206, H.207, R.221, M.254, Y.257, D.291, C.292, Y.429, E.492 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:Y.429, B:R.166, B:R.166, B:K.206, B:H.207, B:R.221, B:Y.257, B:Y.257 Water bridges: B:P.15, B:L.17

1 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-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.8: 11 residues within 4Å: Chain B: D.381, A.382, N.384, Y.387, Y.435, I.437, E.441, S.552, V.555 Ligands: NAG-NAG.9, NAG-NAG.9 No protein-ligand interaction detected (PLIP)

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

NAG.11: 7 residues within 4Å: Chain A: N.3, Q.4, T.5, Y.6, A.7, Y.9, N.300 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.7, A:N.300, A:N.300 Water bridges: A:Y.9 NAG.12: 5 residues within 4Å: Chain A: Y.6, N.8, S.10, A.11, N.218 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.8, A:N.218 NAG.13: 2 residues within 4Å: Chain A: N.217, N.218 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.218 NAG.14: 4 residues within 4Å: Chain B: A.305, S.306, N.307, S.310 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.306, B:S.310 Water bridges: B:E.340 NAG.15: 4 residues within 4Å: Chain A: N.637, S.639, S.640, G.755 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.637, A:S.640 NAG.21: 7 residues within 4Å: Chain B: N.3, Q.4, T.5, Y.6, A.7, Y.9, N.300 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:A.7, B:N.300, B:N.300 Water bridges: B:Y.9 NAG.22: 5 residues within 4Å: Chain B: Y.6, N.8, S.10, A.11, N.218 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:Y.6 Hydrogen bonds: B:N.8, B:N.218 NAG.23: 4 residues within 4Å: Chain A: A.305, S.306, N.307, S.310 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.306, A:N.307, A:S.310 Water bridges: A:E.340 NAG.24: 1 residues within 4Å: Chain B: N.461 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.461 NAG.25: 4 residues within 4Å: Chain B: N.637, S.639, S.640, G.755 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.637

12 x ZN: ZINC ION(Non-covalent)

ZN.16: 2 residues within 4Å: Chain A: D.31, H.34 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.31, A:D.31, A:H.34, H2O.2 ZN.17: 1 residues within 4Å: Chain A: H.34 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.34, H2O.20, H2O.20 ZN.18: 1 residues within 4Å: Chain A: H.128 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:H.128, H2O.6, H2O.6, H2O.6, H2O.20 ZN.19: 2 residues within 4Å: Chain A: E.197, H.198 5 PLIP interactions: 5 Ligand-Water interactions Metal complexes: H2O.8, H2O.8, H2O.8, H2O.8, H2O.8 ZN.20: 2 residues within 4Å: Chain A: H.331, E.334 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.331, A:E.334, A:E.334, H2O.11, H2O.11 ZN.26: 2 residues within 4Å: Chain B: D.31, H.34 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.31, B:D.31, B:H.34, H2O.22, H2O.22 ZN.27: 1 residues within 4Å: Chain B: H.128 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:H.128, H2O.25, H2O.25, H2O.25, H2O.37 ZN.28: 2 residues within 4Å: Chain B: E.197, H.198 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:H.198, H2O.27, H2O.27, H2O.27 ZN.29: 4 residues within 4Å: Chain B: G.223, D.225, S.259, H.302 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.225, B:H.302, H2O.27, H2O.27, H2O.29 ZN.30: 1 residues within 4Å: Chain B: D.303 No protein-ligand interaction detected (PLIP) ZN.31: 2 residues within 4Å: Chain B: H.331, E.334 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.331, B:E.334, B:E.334, H2O.30, H2O.30 ZN.32: 1 residues within 4Å: Chain B: H.582 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:H.582, H2O.34, H2O.34, H2O.37, H2O.37

Links

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Citation

Mikkelsen, N.E. et al., Th Crystal Structure of a Fungal Glycoside Hydrolase Family 3 Beta-Xylosidase, Xyl3A from Hypocrea Jecorina. To be Published

Release Date

2016-09-21

Peptides

BETA-XYLOSIDASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

BETA-XYLOSIDASE