SMTL ID : 5a7m.2 (1 other biounit)

The structure of Hypocrea jecorina beta-xylosidase Xyl3A (Bxl1)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

monomer

Ligands

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.1: 9 residues within 4Å: Chain A: N.123, T.125, L.126, Q.129, W.383, E.392, R.700, L.701, A.702 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.129, A:Q.129

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.2: 3 residues within 4Å: Chain A: W.330, N.333, E.334 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:W.330

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.3: 12 residues within 4Å: Chain A: D.381, A.382, N.384, Y.387, Y.435, L.436, I.437, E.441, K.445, S.552 Ligands: NAG-NAG.4, NAG-NAG.4 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.445, A:K.445, A:E.441

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

NAG-NAG.4: 6 residues within 4Å: Chain A: N.420, T.422, L.440, F.452 Ligands: NAG-NAG-BMA-MAN-MAN.3, NAG-NAG-BMA-MAN-MAN.3 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 4 residues within 4Å: Chain A: N.637, S.639, S.640, G.755 No protein-ligand interaction detected (PLIP)

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

NAG.6: 7 residues within 4Å: Chain A: N.3, Q.4, T.5, Y.6, A.7, Y.9, N.300 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:N.3, A:A.7, A:N.300, A:N.300 Water bridges: A:N.3, A:N.3, A:Y.9, A:Y.296 NAG.7: 3 residues within 4Å: Chain A: Y.6, N.8, S.10 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Y.6, A:Y.6 Water bridges: A:N.8, A:N.8, A:N.8, A:N.218 NAG.8: 1 residues within 4Å: Chain A: N.461 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.461

11 x ZN: ZINC ION(Non-covalent)

ZN.9: 2 residues within 4Å: Chain A: D.31, H.34 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.31, A:H.34, H2O.4, H2O.4, H2O.4 ZN.10: 2 residues within 4Å: Chain A: D.95 Ligands: ACT.23 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.95, A:D.95, H2O.8, H2O.8 ZN.11: 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.10, H2O.10, H2O.10, H2O.36 ZN.12: 2 residues within 4Å: Chain A: H.128, E.185 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:E.185, H2O.10, H2O.10, H2O.14, H2O.37 ZN.13: 1 residues within 4Å: Chain A: H.198 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:H.198, H2O.14, H2O.15, H2O.15, H2O.37 ZN.14: 4 residues within 4Å: Chain A: G.223, D.225, S.259, H.302 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.225, A:D.225, A:H.302, H2O.16, H2O.16 ZN.15: 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.19, H2O.20 ZN.16: 2 residues within 4Å: Chain A: H.449, N.451 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:H.449, H2O.24, H2O.24, H2O.24 ZN.17: 2 residues within 4Å: Chain A: T.497, H.582 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:H.582, H2O.26, H2O.26, H2O.26 ZN.18: 1 residues within 4Å: Chain A: H.582 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:H.582, H2O.28, H2O.28, H2O.28 ZN.19: 1 residues within 4Å: Chain A: H.708 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.708

1 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.20: 10 residues within 4Å: Chain A: Q.14, P.15, W.87, R.221, Y.257, C.292, Y.429, E.492 Ligands: GOL.21, ACT.23 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:Q.14, A:Q.14, A:R.221, A:R.221, A:Y.257, A:Y.257, A:E.492, A:E.492 Water bridges: A:R.166

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.21: 10 residues within 4Å: Chain A: E.89, Y.152, R.166, K.206, H.207, M.254, D.291, C.292, Y.429 Ligands: TRS.20 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:E.89, A:R.166, A:R.166, A:H.207, A:C.292 Water bridges: A:K.206, A:Y.257 GOL.22: 2 residues within 4Å: Chain A: H.727, N.729 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.729 Water bridges: A:H.727, A:W.763

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.23: 5 residues within 4Å: Chain A: D.95, R.96, Y.429 Ligands: ZN.10, TRS.20 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.429 Water bridges: A:Y.429 Salt bridges: A:R.96

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

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

2016-08-10

Peptides

BETA-XYLOSIDASE: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

BETA-XYLOSIDASE

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