SMTL ID : 4uoj.1 (1 other biounit)

Structure of Fungal beta-mannosidase (GH2) from Trichoderma harzianum

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

monomer

Ligands

1 x NAG- NAG- BMA- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(2-6)]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: 15 residues within 4Å: Chain A: D.456, P.507, Y.508, L.510, G.511, Q.512, E.514, N.515, V.552, V.555, E.556, R.557, Y.558, Y.559, N.560 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.514, A:E.514

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

NAG-NAG-MAN.2: 9 residues within 4Å: Chain A: F.617, N.618, V.646, T.649, L.650, E.653, W.671 Ligands: NAG-NAG.3, NAG-NAG.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.653

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

NAG-NAG.3: 9 residues within 4Å: Chain A: E.653, P.659, D.660, K.661, N.667, W.671 Ligands: NAG-NAG-MAN.2, NAG-NAG-MAN.2, CD.12 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- BMA- MAN- MAN- MAN- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-beta-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-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(Post Translational Modification)

NAG-NAG-BMA-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.4: 22 residues within 4Å: Chain A: F.236, N.255, S.257, D.259, T.293, Q.294, S.295, M.297, T.298, T.300, V.465, G.466, T.469, R.473, N.523, A.527, N.528, H.530, L.548, D.549, L.550, P.551 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.523, A:L.548, A:T.469 Water bridges: A:R.133, A:R.133, A:R.133, A:R.133, A:G.466

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

NAG-NAG-MAN-MAN-MAN-MAN-MAN-MAN.5: 16 residues within 4Å: Chain A: E.43, N.86, Y.115, A.116, T.117, D.122, H.123, I.124, V.125, G.126, T.127, D.129, N.155, F.156, G.157, I.162 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.122, A:I.124, A:T.117 Hydrophobic interactions: A:Y.115

1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(3-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.6: 3 residues within 4Å: Chain A: N.357, L.544, R.557 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.544

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

NAG.7: 2 residues within 4Å: Chain A: Y.44, N.46 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.46 Water bridges: A:N.46 NAG.8: 5 residues within 4Å: Chain A: N.167, A.168, H.174, P.186, N.187 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:P.186 Hydrogen bonds: A:N.167, A:N.187 NAG.9: 7 residues within 4Å: Chain A: Y.181, Y.629, P.630, A.631, N.637, N.640, L.643 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Y.629 Hydrogen bonds: A:Y.181, A:Y.181, A:N.637 Water bridges: A:N.640 NAG.10: 2 residues within 4Å: Chain A: R.699, N.799 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.799 Water bridges: A:R.699, A:T.800 NAG.11: 4 residues within 4Å: Chain A: A.277, N.325, Q.343, R.345 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:A.277, A:N.325, A:Q.343, A:R.345 Water bridges: A:D.434, A:D.434

16 x CD: CADMIUM ION(Non-covalent)

CD.12: 2 residues within 4Å: Chain A: D.660 Ligands: NAG-NAG.3 Ligand excluded by PLIP CD.13: 1 residues within 4Å: Chain A: E.438 Ligand excluded by PLIP CD.14: 1 residues within 4Å: Chain A: D.296 Ligand excluded by PLIP CD.15: 2 residues within 4Å: Chain A: E.752, D.811 Ligand excluded by PLIP CD.16: 3 residues within 4Å: Chain A: I.367, E.381, R.699 Ligand excluded by PLIP CD.17: 1 residues within 4Å: Chain A: N.72 Ligand excluded by PLIP CD.18: 1 residues within 4Å: Chain A: D.611 Ligand excluded by PLIP CD.19: 1 residues within 4Å: Chain A: H.62 Ligand excluded by PLIP CD.20: 1 residues within 4Å: Chain A: E.412 Ligand excluded by PLIP CD.21: 2 residues within 4Å: Chain A: D.430, D.434 Ligand excluded by PLIP CD.22: 5 residues within 4Å: Chain A: R.344, D.430, R.474, H.477, H.478 Ligand excluded by PLIP CD.23: 1 residues within 4Å: Chain A: N.75 Ligand excluded by PLIP CD.24: 1 residues within 4Å: Chain A: E.913 Ligand excluded by PLIP CD.25: 1 residues within 4Å: Chain A: E.613 Ligand excluded by PLIP CD.26: 2 residues within 4Å: Chain A: D.306, H.308 Ligand excluded by PLIP CD.31: 1 residues within 4Å: Chain A: D.571 Ligand excluded by PLIP

2 x NA: SODIUM ION(Non-functional Binders)

NA.27: 1 residues within 4Å: Chain A: H.565 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.565 NA.28: 4 residues within 4Å: Chain A: W.422, N.488, E.489, E.594 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.488, A:E.489

1 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.29: 4 residues within 4Å: Chain A: P.397, V.399, W.431 Ligands: PE4.30 3 PLIP interactions: 3 interactions with chain A Water bridges: A:Q.213, A:S.401, A:S.401

1 x PE4: 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL(Non-functional Binders)

PE4.30: 9 residues within 4Å: Chain A: K.52, P.54, S.55, L.59, D.60, P.397, R.398, T.400 Ligands: 1PE.29 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.60 Water bridges: A:A.63

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nascimento, A.S. et al., Insights Into the Structure and Function of Fungal Beta-Mannosidases from Glycoside Hydrolase Family 2 Based on Multiple Crystal Structures of the Trichoderma Harzianum Enzyme. FEBS J. (2014)

Release Date

2014-07-09

Peptides

BETA-MANNOSIDASE GH2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

BETA-MANNOSIDASE GH2

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