SMTL ID : 4cvu.1

Structure of Fungal beta-mannosidase from Glycoside Hydrolase Family 2 of Trichoderma harzianum

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

2 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: F.617, N.618, T.642, V.646, T.649, L.650, E.653, W.671 Ligands: NAG.7 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.653 NAG-NAG-BMA.39: 9 residues within 4Å: Chain B: F.617, N.618, T.642, V.646, T.649, L.650, E.653, W.671 Ligands: NAG.45 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.653

2 x NAG- NAG- BMA- 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)]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-MAN-MAN-MAN-MAN-MAN.2: 17 residues within 4Å: Chain A: E.43, N.86, Y.115, A.116, T.117, D.122, H.123, I.124, G.126, T.127, D.129, N.155, F.156, G.157, I.162, I.166 Ligands: NA.30 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.117, A:D.122, A:I.124 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.40: 17 residues within 4Å: Chain B: E.43, N.86, Y.115, A.116, T.117, D.122, H.123, I.124, G.126, T.127, D.129, N.155, F.156, G.157, I.162, I.166 Ligands: NA.68 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.122, B:H.123, B:I.124

2 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(Post Translational Modification)

NAG-NAG-BMA-MAN-MAN-MAN.3: 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 NAG-NAG-BMA-MAN-MAN-MAN.41: 15 residues within 4Å: Chain B: 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 B Hydrogen bonds: B:E.514, B:E.514

2 x NAG- NAG- BMA- MAN- 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-(1-3)-[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-MAN-MAN-MAN-MAN-MAN-MAN-MAN-MAN.4: 21 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, L.550, P.551 4 PLIP interactions: 4 interactions with chain A Water bridges: A:N.523, A:A.527, A:R.473, A:R.133, A:R.133 Hydrogen bonds: A:G.466, A:T.469 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN-MAN.42: 21 residues within 4Å: Chain B: 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, L.550, P.551 3 PLIP interactions: 3 interactions with chain B Water bridges: B:N.523, B:A.527, B:R.473, B:R.133, B:R.133 Hydrogen bonds: B:G.466

14 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)(Non-covalent)

NAG.5: 5 residues within 4Å: Chain A: N.357, L.544, E.545, R.557 Ligands: NAG.6 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.357, A:L.544, A:E.545, A:R.557, A:R.557 Water bridges: A:E.545 NAG.6: 2 residues within 4Å: Chain A: L.544 Ligands: NAG.5 No protein-ligand interaction detected (PLIP) NAG.7: 5 residues within 4Å: Chain A: D.660, K.661, N.667, W.671 Ligands: NAG-NAG-BMA.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.660, A:D.660, A:N.667 NAG.8: 3 residues within 4Å: Chain A: Y.44, N.46, I.47 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:I.47 NAG.9: 6 residues within 4Å: Chain A: N.167, A.168, D.170, H.174, P.186, N.187 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:P.186 Hydrogen bonds: A:N.167, A:D.170, A:D.170, A:N.187 Water bridges: A:N.167 NAG.10: 2 residues within 4Å: Chain A: R.699, N.799 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.799 Water bridges: A:R.699 NAG.11: 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.43: 5 residues within 4Å: Chain B: N.357, L.544, E.545, R.557 Ligands: NAG.44 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.357, B:L.544, B:E.545, B:R.557, B:R.557 NAG.44: 2 residues within 4Å: Chain B: L.544 Ligands: NAG.43 No protein-ligand interaction detected (PLIP) NAG.45: 5 residues within 4Å: Chain B: D.660, K.661, N.667, W.671 Ligands: NAG-NAG-BMA.39 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.660, B:D.660, B:D.660, B:N.667 NAG.46: 3 residues within 4Å: Chain B: Y.44, N.46, I.47 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:I.47 NAG.47: 6 residues within 4Å: Chain B: N.167, A.168, D.170, H.174, P.186, N.187 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:P.186 Hydrogen bonds: B:N.167, B:D.170, B:N.187 Water bridges: B:N.167 NAG.48: 2 residues within 4Å: Chain B: R.699, N.799 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.799 Water bridges: B:R.699 NAG.49: 7 residues within 4Å: Chain B: Y.181, Y.629, P.630, A.631, N.637, N.640, L.643 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:Y.629 Hydrogen bonds: B:Y.181, B:N.637 Water bridges: B:N.640

34 x CD: CADMIUM ION(Non-covalent)

CD.12: 2 residues within 4Å: Chain A: H.62 Chain B: E.613 Ligand excluded by PLIP CD.13: 2 residues within 4Å: Chain A: N.72 Chain B: D.611 Ligand excluded by PLIP CD.14: 1 residues within 4Å: Chain A: N.75 Ligand excluded by PLIP CD.15: 2 residues within 4Å: Chain A: D.547, D.549 Ligand excluded by PLIP CD.16: 1 residues within 4Å: Chain A: D.660 Ligand excluded by PLIP CD.17: 2 residues within 4Å: Chain A: D.430, D.434 Ligand excluded by PLIP CD.18: 5 residues within 4Å: Chain A: R.344, D.430, R.474, H.477, H.478 Ligand excluded by PLIP CD.19: 1 residues within 4Å: Chain A: E.412 Ligand excluded by PLIP CD.20: 2 residues within 4Å: Chain A: E.381, R.699 Ligand excluded by PLIP CD.21: 1 residues within 4Å: Chain A: E.438 Ligand excluded by PLIP CD.22: 2 residues within 4Å: Chain A: D.571 Ligands: NA.38 Ligand excluded by PLIP CD.23: 1 residues within 4Å: Chain A: D.296 Ligand excluded by PLIP CD.24: 2 residues within 4Å: Chain A: H.848, V.905 Ligand excluded by PLIP CD.25: 2 residues within 4Å: Chain A: E.825, R.907 Ligand excluded by PLIP CD.26: 2 residues within 4Å: Chain A: E.752, D.811 Ligand excluded by PLIP CD.27: 2 residues within 4Å: Chain A: D.306, H.308 Ligand excluded by PLIP CD.28: 1 residues within 4Å: Chain A: D.402 Ligand excluded by PLIP CD.50: 2 residues within 4Å: Chain A: E.613 Chain B: H.62 Ligand excluded by PLIP CD.51: 2 residues within 4Å: Chain A: D.611 Chain B: N.72 Ligand excluded by PLIP CD.52: 1 residues within 4Å: Chain B: N.75 Ligand excluded by PLIP CD.53: 2 residues within 4Å: Chain B: D.547, D.549 Ligand excluded by PLIP CD.54: 1 residues within 4Å: Chain B: D.660 Ligand excluded by PLIP CD.55: 2 residues within 4Å: Chain B: D.430, D.434 Ligand excluded by PLIP CD.56: 5 residues within 4Å: Chain B: R.344, D.430, R.474, H.477, H.478 Ligand excluded by PLIP CD.57: 1 residues within 4Å: Chain B: E.412 Ligand excluded by PLIP CD.58: 2 residues within 4Å: Chain B: E.381, R.699 Ligand excluded by PLIP CD.59: 1 residues within 4Å: Chain B: E.438 Ligand excluded by PLIP CD.60: 2 residues within 4Å: Chain B: D.571 Ligands: NA.76 Ligand excluded by PLIP CD.61: 1 residues within 4Å: Chain B: D.296 Ligand excluded by PLIP CD.62: 2 residues within 4Å: Chain B: H.848, V.905 Ligand excluded by PLIP CD.63: 2 residues within 4Å: Chain B: E.825, R.907 Ligand excluded by PLIP CD.64: 2 residues within 4Å: Chain B: E.752, D.811 Ligand excluded by PLIP CD.65: 2 residues within 4Å: Chain B: D.306, H.308 Ligand excluded by PLIP CD.66: 1 residues within 4Å: Chain B: D.402 Ligand excluded by PLIP

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

NA.29: 1 residues within 4Å: Chain A: E.754 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.754 NA.30: 2 residues within 4Å: Chain A: D.129 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.2 1 PLIP interactions: 1 interactions with chain A Water bridges: A:D.459 NA.31: 1 residues within 4Å: Chain A: D.409 1 PLIP interactions: 1 interactions with chain A Water bridges: A:D.409 NA.32: 2 residues within 4Å: Chain A: D.502, T.505 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.505, A:T.505 NA.33: 1 residues within 4Å: Chain A: A.504 1 PLIP interactions: 1 interactions with chain A Water bridges: A:A.504 NA.38: 1 residues within 4Å: Ligands: CD.22 2 PLIP interactions: 2 interactions with chain A Water bridges: A:D.571, A:D.571 NA.67: 1 residues within 4Å: Chain B: E.754 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.754 NA.68: 2 residues within 4Å: Chain B: D.129 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.40 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.129 NA.69: 1 residues within 4Å: Chain B: D.409 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.409 NA.70: 2 residues within 4Å: Chain B: D.502, T.505 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.502, B:T.505 NA.71: 1 residues within 4Å: Chain B: A.504 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:A.504 NA.76: 1 residues within 4Å: Ligands: CD.60 2 PLIP interactions: 2 interactions with chain B Water bridges: B:N.541, B:D.571

2 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.34: 6 residues within 4Å: Chain A: P.54, S.55, D.60, P.397, R.398, T.400 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.60 PG4.72: 6 residues within 4Å: Chain B: P.54, S.55, D.60, P.397, R.398, T.400 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.60, B:D.60

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.35: 4 residues within 4Å: Chain A: P.397, V.399, T.400, W.431 2 PLIP interactions: 2 interactions with chain A Water bridges: A:S.401, A:S.401 PEG.73: 4 residues within 4Å: Chain B: P.397, V.399, T.400, W.431 2 PLIP interactions: 2 interactions with chain B Water bridges: B:S.401, B:S.401

2 x CA: CALCIUM ION(Non-covalent)

CA.36: 1 residues within 4Å: Chain A: E.614 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.614, A:E.614, H2O.12, H2O.20 CA.74: 1 residues within 4Å: Chain B: E.614 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.614, B:E.614, H2O.41, H2O.49

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.37: 1 residues within 4Å: Chain A: H.565 Ligand excluded by PLIP CL.75: 1 residues within 4Å: Chain B: H.565 Ligand excluded by PLIP

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: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

BETA-MANNOSIDASE

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