SMTL ID : 5a7m.1 (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- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[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.1: 14 residues within 4Å: Chain A: N.123, T.125, L.126, Q.129, A.382, W.383, N.384, I.385, E.388, E.392, R.700, L.701, A.702 Ligands: NAG-NAG-BMA-MAN-MAN.3 3 PLIP interactions: 3 interactions with chain A Water bridges: A:W.383, A:R.565 Hydrogen bonds: A:Q.129, A:Q.129

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.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: 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)

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: 13 residues within 4Å: Chain A: D.381, A.382, N.384, Y.387, Y.435, L.436, I.437, E.441, S.552, V.555 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN.1, NAG-NAG.4, NAG-NAG.4 2 PLIP interactions: 2 interactions with chain A Water bridges: A:N.420, A:E.441, A:E.441

5 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)(Non-functional Binders)

NAG.5: 6 residues within 4Å: Chain A: N.3, Q.4, T.5, Y.6, A.7, N.300 7 PLIP interactions: 7 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 NAG.6: 6 residues within 4Å: Chain A: Y.6, N.8, S.10, A.11, N.218, Q.219 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.8, A:N.218, A:Q.219 NAG.7: 2 residues within 4Å: Chain A: N.217, N.218 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.218 Water bridges: A:N.218, A:N.218 NAG.8: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) NAG.9: 4 residues within 4Å: Chain A: N.637, S.639, S.640, G.755 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.637, A:S.640 Water bridges: A:N.637, A:S.639

10 x ZN: ZINC ION(Non-covalent)

ZN.10: 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.4 ZN.11: 2 residues within 4Å: Chain A: E.33, H.34 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:H.34, H2O.4, H2O.4, H2O.4, H2O.37 ZN.12: 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.13: 1 residues within 4Å: Chain A: H.128 6 PLIP interactions: 1 interactions with chain A, 5 Ligand-Water interactions Metal complexes: A:H.128, H2O.10, H2O.10, H2O.10, H2O.10, H2O.37 ZN.14: 5 residues within 4Å: Chain A: G.223, D.225, S.259, H.302 Ligands: ZN.15 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.225, A:D.225, A:H.302, H2O.15, H2O.15 ZN.15: 2 residues within 4Å: Chain A: D.225 Ligands: ZN.14 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.225, H2O.15, H2O.15, H2O.15, H2O.37 ZN.16: 1 residues within 4Å: Chain A: E.278 No protein-ligand interaction detected (PLIP) ZN.17: 2 residues within 4Å: Chain A: H.331, E.334 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.331, A:E.334, A:E.334, H2O.20 ZN.18: 2 residues within 4Å: Chain A: E.671, K.705 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.671, H2O.33, H2O.33, H2O.33 ZN.19: 1 residues within 4Å: Chain A: H.708 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:H.708, H2O.34, H2O.34, H2O.34, H2O.37

2 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.22, ACT.23 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:Q.14, A:Q.14, A:R.221, A:R.221, A:Y.257, A:Y.429, A:E.492 Water bridges: A:R.166 TRS.21: 1 residues within 4Å: Chain A: N.762 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.729, A:T.759, A:N.762, A:N.762 Water bridges: A:N.729

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.22: 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 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.166, A:R.166, A:K.206, A:H.207, A:C.292 Water bridges: A:K.206

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

ACT.23: 5 residues within 4Å: Chain A: D.95, R.96, Y.429 Ligands: ZN.12, 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
A

BETA-XYLOSIDASE

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