SMTL ID : 5ju6.1

Structural and Functional Studies of Glycoside Hydrolase Family 3 beta-Glucosidase Cel3A from the Moderately Thermophilic Fungus Rasamsonia emersonii

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-tetramer

Ligands

2 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.1: 15 residues within 4Å: Chain A: A.57, E.58, N.61, G.78, S.79, I.80, P.81, H.364, D.694, I.695, E.696, V.698, Y.701, Y.703, W.705 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.694, A:Y.703 Hydrophobic interactions: A:V.698, A:Y.701 NAG-NAG-BMA-MAN-MAN.9: 13 residues within 4Å: Chain B: Y.24, S.25, P.26, A.217, D.218, D.219, V.248, N.249, Y.258, T.259, P.822, V.823, T.824 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.219, B:Y.258

1 x NAG- NAG- BMA- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-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.2: 14 residues within 4Å: Chain A: Y.24, S.25, P.26, A.217, D.218, D.219, V.248, N.249, Y.258, T.259, P.822, V.823, T.824, Q.825 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:D.218 Hydrogen bonds: A:D.219, A:Y.258

4 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.3: 14 residues within 4Å: Chain A: I.300, T.306, S.307, F.308, T.311, N.312, S.714, A.715, N.716, D.717, P.718 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.4, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.4, NAG.32 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.716 NAG-NAG-BMA-MAN.8: 15 residues within 4Å: Chain B: A.57, E.58, N.61, G.78, S.79, I.80, P.81, H.364, D.694, I.695, V.698, Y.701, Y.703, W.705 Ligands: MAN.35 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:V.698, B:Y.701 Hydrogen bonds: B:D.694, B:Y.703 NAG-NAG-BMA-MAN.10: 11 residues within 4Å: Chain B: I.300, T.306, S.307, F.308, N.312, S.714, A.715, N.716, D.717, P.718 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.11 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:F.308 Hydrogen bonds: B:N.716 NAG-NAG-BMA-MAN.25: 13 residues within 4Å: Chain D: I.300, T.306, S.307, F.308, T.311, N.312, S.714, A.715, N.716, D.717, P.718 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.26, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.26 1 PLIP interactions: 1 interactions with chain D Water bridges: D:N.716

2 x NAG- NAG- BMA- MAN- MAN- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]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

NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.4: 31 residues within 4Å: Chain A: Y.24, S.25, P.26, P.27, Y.29, D.211, N.250, S.251, S.255, H.282, S.283, G.284, V.285, G.286, F.308, N.312, V.315, A.316, N.319, S.321, A.715, D.717, D.719, Y.720, G.721, L.722, Y.727, V.728, P.729 Ligands: NAG-NAG-BMA-MAN.3, NAG-NAG-BMA-MAN.3 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.719, A:G.284, A:V.285, A:D.717, A:G.721, A:L.722 Water bridges: A:G.286 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.18: 31 residues within 4Å: Chain C: Y.24, S.25, P.26, P.27, Y.29, N.250, S.251, S.255, H.282, S.283, G.284, V.285, G.286, F.308, N.312, V.315, A.316, N.319, S.321, A.715, D.717, D.719, Y.720, G.721, L.722, K.726, Y.727, V.728, P.729 Ligands: NAG-NAG-BMA-MAN-MAN.17, NAG-NAG-BMA-MAN-MAN.17 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:D.719, C:D.719, C:K.726, C:G.284, C:V.285, C:D.717, C:D.717, C:D.719, C:G.721, C:L.722 Water bridges: C:G.286

1 x NAG- NAG- BMA- MAN: 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.5: 8 residues within 4Å: Chain A: P.425, W.426, C.431, G.435, C.436, N.438 Chain B: D.478 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.13 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- 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-(1-6)-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

NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.6: 15 residues within 4Å: Chain A: D.478, G.480, A.481, E.484, D.511, N.513, K.518, N.519, T.521, W.523, Q.524, G.525 Chain B: W.426 Ligands: NAG-NAG-BMA-BMA-MAN.12, NAG.30 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:E.484, A:D.511, A:Q.524 Water bridges: A:L.482, A:A.483, A:G.525, A:G.525, A:G.525, A:G.525, A:D.527 Hydrophobic interactions: A:D.511

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

NAG-NAG.7: 6 residues within 4Å: Chain A: S.534, A.535, N.536, N.538, H.558, N.560 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 8 residues within 4Å: Chain B: S.534, A.535, N.536, C.537, N.538, H.558, P.559, N.560 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 1 residues within 4Å: Chain C: N.538 No protein-ligand interaction detected (PLIP)

2 x NAG- NAG- BMA- MAN- MAN- MAN- MAN- MAN- MAN- MAN: 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)-[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-MAN-MAN-MAN-MAN-MAN.11: 28 residues within 4Å: Chain B: Y.24, S.25, P.26, P.27, Y.29, S.251, S.255, H.282, S.283, G.284, V.285, G.286, F.308, N.312, V.315, A.316, N.319, S.321, A.715, D.717, D.719, Y.720, G.721, L.722, Y.727, V.728, P.729 Ligands: NAG-NAG-BMA-MAN.10 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:D.719, B:G.284, B:V.285, B:D.717, B:G.721, B:L.722 Hydrophobic interactions: B:N.312 Water bridges: B:G.286 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.26: 30 residues within 4Å: Chain D: Y.24, S.25, P.26, P.27, Y.29, S.251, S.255, H.282, S.283, G.284, V.285, G.286, F.308, N.312, V.315, A.316, N.319, S.321, A.715, D.717, D.719, Y.720, G.721, L.722, K.726, Y.727, V.728, P.729 Ligands: NAG-NAG-BMA-MAN.25, NAG-NAG-BMA-MAN.25 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:D.719, D:D.719, D:K.726, D:G.284, D:V.285, D:D.717, D:D.719, D:G.721, D:L.722, D:L.722

1 x NAG- NAG- BMA- BMA- MAN: beta-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-BMA-MAN.12: 6 residues within 4Å: Chain A: D.478 Chain B: W.426, C.436, N.438 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.6, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.13 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- 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-(1-6)-[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-MAN-MAN-MAN.13: 17 residues within 4Å: Chain A: W.426 Chain B: D.478, G.480, A.481, E.484, D.511, N.513, K.518, N.519, T.521, W.523, Q.524, G.525, Q.528 Ligands: NAG-NAG-BMA-MAN.5, NAG-NAG-BMA-BMA-MAN.12, NAG.36 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Q.528, B:D.511, B:Q.524, B:G.525 Hydrophobic interactions: B:D.511, B:W.523

1 x NAG- NAG- BMA- 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-(1-6)]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-MAN-MAN.15: 17 residues within 4Å: Chain C: A.57, E.58, N.61, G.78, S.79, I.80, P.81, H.364, G.370, T.372, D.694, I.695, E.696, V.698, Y.701, Y.703, W.705 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:V.698, C:Y.701

2 x NAG- NAG- BMA- MAN- MAN- MAN- GLC- MAN: alpha-D-glucopyranose-(1-3)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-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-GLC-MAN.16: 14 residues within 4Å: Chain C: Y.24, S.25, P.26, A.217, D.218, D.219, V.248, N.249, Y.258, T.259, P.822, V.823, T.824, Q.825 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:D.218 Hydrogen bonds: C:D.219, C:Y.258 Water bridges: C:K.220 NAG-NAG-BMA-MAN-MAN-MAN-GLC-MAN.24: 14 residues within 4Å: Chain D: Y.24, S.25, P.26, A.217, D.218, D.219, V.248, N.249, Y.258, T.259, P.822, V.823, T.824, Q.825 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:D.219, D:Y.258, D:Q.825 Water bridges: D:K.220

1 x NAG- NAG- BMA- MAN- MAN: 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.17: 12 residues within 4Å: Chain C: I.300, T.306, S.307, F.308, N.312, S.714, A.715, N.716, D.717, P.718 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.18, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.18 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.716

3 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.19: 7 residues within 4Å: Chain C: P.425, W.426, G.435, C.436, N.438 Chain D: D.478 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.28 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.22: 8 residues within 4Å: Chain C: S.534, A.535, N.536, C.537, N.538, H.558, P.559, N.560 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.27: 7 residues within 4Å: Chain C: D.478 Chain D: P.425, W.426, C.431, C.436, N.438 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.20 No protein-ligand interaction detected (PLIP)

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

NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.20: 15 residues within 4Å: Chain C: G.480, A.481, L.482, E.484, D.511, N.513, K.518, N.519, T.521, W.523, Q.524, G.525, Q.528 Chain D: W.426 Ligands: NAG-NAG-BMA.27 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:D.511 Hydrogen bonds: C:D.511, C:Q.524 Water bridges: C:K.419, C:D.511, C:G.525, C:G.525 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.28: 15 residues within 4Å: Chain C: W.426 Chain D: D.478, G.480, A.481, L.482, E.484, D.511, N.513, K.518, N.519, T.521, W.523, Q.524, G.525 Ligands: NAG-NAG-BMA.19 10 PLIP interactions: 10 interactions with chain D Hydrophobic interactions: D:D.511, D:W.523 Hydrogen bonds: D:D.511, D:D.511, D:Q.524 Water bridges: D:G.525, D:G.525, D:G.525, D:A.526, D:D.527

1 x NAG- NAG- BMA- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-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.23: 15 residues within 4Å: Chain D: A.57, E.58, N.61, G.78, S.79, I.80, P.81, H.364, Q.371, I.695, E.696, V.698, Y.701, Y.703, W.705 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:V.698, D:Y.701

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

NAG.29: 6 residues within 4Å: Chain A: R.469, N.470 Chain B: G.382, N.383 Chain C: R.123, E.390 Ligand excluded by PLIP NAG.30: 5 residues within 4Å: Chain A: L.482, A.483, Q.528, N.532 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.6 Ligand excluded by PLIP NAG.31: 1 residues within 4Å: Chain A: N.538 Ligand excluded by PLIP NAG.32: 5 residues within 4Å: Chain A: N.707, A.713, S.714, N.716 Ligands: NAG-NAG-BMA-MAN.3 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain A: P.730, N.731 Ligand excluded by PLIP NAG.36: 5 residues within 4Å: Chain B: L.482, A.483, A.486, N.532 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.13 Ligand excluded by PLIP NAG.37: 1 residues within 4Å: Chain B: N.636 Ligand excluded by PLIP NAG.38: 2 residues within 4Å: Chain B: P.730, N.731 Ligand excluded by PLIP NAG.40: 6 residues within 4Å: Chain A: R.123, E.390 Chain C: N.470 Chain D: G.382, N.383, A.385 Ligand excluded by PLIP NAG.41: 5 residues within 4Å: Chain C: L.482, A.483, A.486, Q.528, N.532 Ligand excluded by PLIP NAG.42: 2 residues within 4Å: Chain C: N.636, T.638 Ligand excluded by PLIP NAG.44: 4 residues within 4Å: Chain D: L.482, A.483, Q.528, N.532 Ligand excluded by PLIP NAG.45: 1 residues within 4Å: Chain D: N.538 Ligand excluded by PLIP NAG.46: 6 residues within 4Å: Chain D: S.534, A.535, C.537, N.538, H.558, N.560 Ligand excluded by PLIP NAG.47: 4 residues within 4Å: Chain D: R.697, N.707, S.714, N.716 Ligand excluded by PLIP NAG.48: 4 residues within 4Å: Chain D: P.730, N.731, N.734, Q.738 Ligand excluded by PLIP

4 x BGC: beta-D-glucopyranose(Non-covalent)

BGC.34: 14 residues within 4Å: Chain A: V.74, D.92, R.98, L.141, R.156, K.189, H.190, R.200, M.242, Y.245, D.277, W.278, S.447, E.505 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:R.98, A:R.156, A:R.156, A:K.189, A:H.190, A:H.190, A:R.200, A:R.200, A:Y.245, A:Y.245, A:S.447 Water bridges: A:R.98, A:K.189 BGC.39: 14 residues within 4Å: Chain B: V.74, D.92, R.98, L.141, R.156, K.189, H.190, R.200, M.242, Y.245, D.277, W.278, S.447, E.505 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:R.98, B:R.156, B:R.156, B:K.189, B:H.190, B:H.190, B:R.200, B:R.200, B:Y.245, B:S.447 Water bridges: B:K.189 BGC.43: 14 residues within 4Å: Chain C: V.74, D.92, R.98, L.141, R.156, K.189, H.190, R.200, M.242, Y.245, D.277, W.278, S.447, E.505 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:R.98, C:R.156, C:R.156, C:K.189, C:H.190, C:H.190, C:R.200, C:S.447, C:E.505 BGC.49: 13 residues within 4Å: Chain D: D.92, R.98, L.141, R.156, K.189, H.190, R.200, M.242, Y.245, D.277, W.278, S.447, E.505 10 PLIP interactions: 10 interactions with chain D Hydrogen bonds: D:R.98, D:R.156, D:R.156, D:K.189, D:H.190, D:H.190, D:R.200, D:S.447, D:E.505 Water bridges: D:K.189

1 x MAN: alpha-D-mannopyranose(Non-functional Binders)

MAN.35: 1 residues within 4Å: Ligands: NAG-NAG-BMA-MAN.8 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gudmundsson, M. et al., Structural and functional studies of the glycoside hydrolase family 3 beta-glucosidase Cel3A from the moderately thermophilic fungus Rasamsonia emersonii. Acta Crystallogr D Struct Biol (2016)

Release Date

2016-07-13

Peptides

Beta-glucosidase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Beta-glucosidase