SMTL ID : 6s82.1 (1 other biounit)

Structure Of D80A-Fructofuranosidase From Xanthophyllomyces Dendrorhous Complexed With Tris-buffer molecule And hydroquinone

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-dimer

Ligands

2 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: 10 residues within 4Å: Chain A: N.58, K.405, L.649, V.650, W.651, P.654, Y.665 Chain B: A.202, G.203, Y.209 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Water bridges: A:K.405, B:Y.209 Hydrophobic interactions: B:A.202 Hydrogen bonds: B:G.203, B:Y.209 NAG-NAG-BMA-MAN-MAN-MAN-MAN.30: 10 residues within 4Å: Chain A: A.202, G.203, Y.209 Chain B: N.58, K.405, L.649, V.650, W.651, P.654, Y.665 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Water bridges: B:K.405, A:Y.209 Hydrophobic interactions: A:A.202 Hydrogen bonds: A:G.203, A:Y.209

2 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.2: 19 residues within 4Å: Chain A: N.107, S.127, E.128, K.131, W.134 Chain B: W.134, Q.137, I.138, D.155, Y.187, W.195, I.196, K.197, G.199, Y.200, Q.204 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.31, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.31, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.31 7 PLIP interactions: 5 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:Q.137, A:E.128, A:E.128, B:W.134, B:K.197 Water bridges: B:G.199, B:Y.200, B:Q.204, B:Q.137, B:Q.137, B:W.195 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.31: 19 residues within 4Å: Chain A: W.134, Q.137, I.138, D.155, Y.187, W.195, I.196, K.197, G.199, Y.200, Q.204 Chain B: N.107, S.127, E.128, K.131, W.134 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.2, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.2, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.2 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:Q.137, B:E.128, B:E.128, A:W.134, A:K.197 Water bridges: A:G.199, A:Y.200, A:Q.204, A:Q.137, A:Q.137, A:W.195

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.3: 4 residues within 4Å: Chain A: T.574, N.576, N.591 Ligands: PLQ.10 No protein-ligand interaction detected (PLIP) NAG-NAG.32: 4 residues within 4Å: Chain B: T.574, N.576, N.591 Ligands: PLQ.39 No protein-ligand interaction detected (PLIP)

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

TRS.4: 10 residues within 4Å: Chain A: N.79, Q.97, W.105, F.145, D.146, R.220, D.221, E.303 Ligands: EDO.6, EDO.7 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.79, A:Q.97, A:D.146, A:D.221 TRS.33: 10 residues within 4Å: Chain B: N.79, Q.97, W.105, F.145, D.146, R.220, D.221, E.303 Ligands: EDO.35, EDO.36 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.79, B:Q.97, B:D.146, B:D.221

18 x PLQ: 1,4-benzoquinone(Non-covalent)

PLQ.5: 4 residues within 4Å: Chain A: W.105, W.393 Ligands: EDO.6, EDO.7 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:W.105, A:W.105, A:W.105 Water bridges: A:Q.341 PLQ.8: 2 residues within 4Å: Chain A: Q.341, D.399 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Q.341, A:D.399 Water bridges: A:Q.104 PLQ.9: 6 residues within 4Å: Chain A: A.656, A.657, G.660, L.661, F.662, A.663 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.662 Water bridges: A:G.660 PLQ.10: 6 residues within 4Å: Chain A: F.420, K.422, V.423, V.424, D.592 Ligands: NAG-NAG.3 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:K.422 Water bridges: A:K.422 PLQ.11: 5 residues within 4Å: Chain A: D.123, A.640, R.641, P.642, T.645 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:R.641, A:T.645 Water bridges: A:D.123 PLQ.12: 5 residues within 4Å: Chain A: Y.85, Q.86, R.87, A.88, K.151 1 PLIP interactions: 1 interactions with chain A Water bridges: A:A.88 PLQ.13: 2 residues within 4Å: Chain A: T.545 Ligands: NAG.27 No protein-ligand interaction detected (PLIP) PLQ.14: 5 residues within 4Å: Chain A: L.174, N.175, N.215, H.256 Ligands: NAG.17 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:N.175, A:H.256 Hydrogen bonds: A:N.215 Water bridges: A:H.256 PLQ.15: 8 residues within 4Å: Chain A: E.508, F.509, G.510, E.571, S.572, V.622, V.623, G.624 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:E.508 Hydrogen bonds: A:G.624 PLQ.34: 4 residues within 4Å: Chain B: W.105, W.393 Ligands: EDO.35, EDO.36 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:W.105, B:W.105, B:W.105 Water bridges: B:Q.341 PLQ.37: 2 residues within 4Å: Chain B: Q.341, D.399 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:Q.341, B:D.399 Water bridges: B:Q.104 PLQ.38: 6 residues within 4Å: Chain B: A.656, A.657, G.660, L.661, F.662, A.663 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:F.662 Water bridges: B:G.660 PLQ.39: 6 residues within 4Å: Chain B: F.420, K.422, V.423, V.424, D.592 Ligands: NAG-NAG.32 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:K.422 Water bridges: B:K.422 PLQ.40: 5 residues within 4Å: Chain B: D.123, A.640, R.641, P.642, T.645 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:R.641, B:T.645 Water bridges: B:D.123 PLQ.41: 5 residues within 4Å: Chain B: Y.85, Q.86, R.87, A.88, K.151 1 PLIP interactions: 1 interactions with chain B Water bridges: B:A.88 PLQ.42: 2 residues within 4Å: Chain B: T.545 Ligands: NAG.56 No protein-ligand interaction detected (PLIP) PLQ.43: 5 residues within 4Å: Chain B: L.174, N.175, N.215, H.256 Ligands: NAG.46 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:N.175, B:H.256 Hydrogen bonds: B:N.215 Water bridges: B:H.256 PLQ.44: 8 residues within 4Å: Chain B: E.508, F.509, G.510, E.571, S.572, V.622, V.623, G.624 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:E.508 Hydrogen bonds: B:G.624

4 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.6: 4 residues within 4Å: Chain A: W.105, L.170 Ligands: TRS.4, PLQ.5 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.303 EDO.7: 8 residues within 4Å: Chain A: N.79, D.80, E.303, H.343, Y.376, W.393 Ligands: TRS.4, PLQ.5 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.79, A:D.80, A:H.343 EDO.35: 4 residues within 4Å: Chain B: W.105, L.170 Ligands: TRS.33, PLQ.34 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.303 EDO.36: 8 residues within 4Å: Chain B: N.79, D.80, E.303, H.343, Y.376, W.393 Ligands: TRS.33, PLQ.34 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.79, B:D.80, B:H.343

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

NAG.16: 3 residues within 4Å: Chain A: N.52, T.54, L.55 Ligand excluded by PLIP NAG.17: 4 residues within 4Å: Chain A: N.175, T.214, N.215 Ligands: PLQ.14 Ligand excluded by PLIP NAG.18: 2 residues within 4Å: Chain A: L.233, N.236 Ligand excluded by PLIP NAG.19: 2 residues within 4Å: Chain A: I.240, N.242 Ligand excluded by PLIP NAG.20: 1 residues within 4Å: Chain A: N.319 Ligand excluded by PLIP NAG.21: 7 residues within 4Å: Chain A: E.213, Y.278, L.279, P.281, R.355, N.357, S.359 Ligand excluded by PLIP NAG.22: 4 residues within 4Å: Chain A: P.429, F.435, N.444, G.448 Ligand excluded by PLIP NAG.23: 8 residues within 4Å: Chain A: D.117, T.119, S.120, A.466, A.467, G.470, N.471, V.635 Ligand excluded by PLIP NAG.24: 3 residues within 4Å: Chain A: M.481, N.483, S.485 Ligand excluded by PLIP NAG.25: 4 residues within 4Å: Chain A: S.430, L.511, N.512, E.566 Ligand excluded by PLIP NAG.26: 5 residues within 4Å: Chain A: E.293, S.537, N.539, L.559, K.561 Ligand excluded by PLIP NAG.27: 3 residues within 4Å: Chain A: T.545, N.555 Ligands: PLQ.13 Ligand excluded by PLIP NAG.28: 5 residues within 4Å: Chain A: T.47, S.524, E.525, E.526, N.606 Ligand excluded by PLIP NAG.29: 5 residues within 4Å: Chain A: N.58, A.59, T.60, N.644, S.646 Ligand excluded by PLIP NAG.45: 3 residues within 4Å: Chain B: N.52, T.54, L.55 Ligand excluded by PLIP NAG.46: 4 residues within 4Å: Chain B: N.175, T.214, N.215 Ligands: PLQ.43 Ligand excluded by PLIP NAG.47: 2 residues within 4Å: Chain B: L.233, N.236 Ligand excluded by PLIP NAG.48: 2 residues within 4Å: Chain B: I.240, N.242 Ligand excluded by PLIP NAG.49: 1 residues within 4Å: Chain B: N.319 Ligand excluded by PLIP NAG.50: 7 residues within 4Å: Chain B: E.213, Y.278, L.279, P.281, R.355, N.357, S.359 Ligand excluded by PLIP NAG.51: 4 residues within 4Å: Chain B: P.429, F.435, N.444, G.448 Ligand excluded by PLIP NAG.52: 8 residues within 4Å: Chain B: D.117, T.119, S.120, A.466, A.467, G.470, N.471, V.635 Ligand excluded by PLIP NAG.53: 3 residues within 4Å: Chain B: M.481, N.483, S.485 Ligand excluded by PLIP NAG.54: 4 residues within 4Å: Chain B: S.430, L.511, N.512, E.566 Ligand excluded by PLIP NAG.55: 5 residues within 4Å: Chain B: E.293, S.537, N.539, L.559, K.561 Ligand excluded by PLIP NAG.56: 3 residues within 4Å: Chain B: T.545, N.555 Ligands: PLQ.42 Ligand excluded by PLIP NAG.57: 5 residues within 4Å: Chain B: T.47, S.524, E.525, E.526, N.606 Ligand excluded by PLIP NAG.58: 5 residues within 4Å: Chain B: N.58, A.59, T.60, N.644, S.646 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ramirez-Escudero, M. et al., Deciphering the molecular specificity of phenolic compounds as inhibitors or glycosyl acceptors of beta-fructofuranosidase from Xanthophyllomyces dendrorhous. Sci Rep (2019)

Release Date

2020-04-29

Peptides

Beta-fructofuranosidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Beta-fructofuranosidase

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