SMTL ID : 5ann.2 (1 other biounit)

Structure of fructofuranosidase from Xanthophyllomyces dendrorhous

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.14 Å

Oligo State

homo-dimer

Ligands

2 x NAG- NAG- BMA- MAN- MAN- MAN: alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[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(Non-functional Binders)(Post Translational Modification)

NAG-NAG-BMA-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 1 PLIP interactions: 1 interactions with chain A Water bridges: A:K.405 NAG-NAG-BMA-MAN-MAN-MAN.17: 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 1 PLIP interactions: 1 interactions with chain B Water bridges: B:K.405

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(Post Translational Modification)

NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.2: 18 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 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.18, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.18, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.18 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Water bridges: B:K.197, B:S.136, B:S.136, B:Q.137, B:Q.137, B:W.195, B:G.199 Hydrogen bonds: B:W.134, B:K.197, A:E.128, A:E.128, B:Q.137, B:Y.200 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.18: 18 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 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 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Water bridges: A:K.197, A:S.136, A:S.136, A:Q.137, A:Q.137, A:W.195, A:G.199 Hydrogen bonds: A:W.134, A:K.197, A:Q.137, A:Y.200, B:E.128, B:E.128

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: 3 residues within 4Å: Chain A: T.574, N.576, N.591 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 3 residues within 4Å: Chain B: T.574, N.576, N.591 No protein-ligand interaction detected (PLIP)

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 7 residues within 4Å: Chain A: N.79, D.80, Q.97, W.105, F.145, D.146, D.221 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.79, A:W.105, A:D.146, A:D.146 GOL.16: 10 residues within 4Å: Chain A: Q.86, G.90, I.92, S.116, D.117, F.118, V.383, E.384, R.387, E.463 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.86, A:S.116, A:E.384 Water bridges: A:E.384, A:R.387 GOL.20: 7 residues within 4Å: Chain B: N.79, D.80, Q.97, W.105, F.145, D.146, D.221 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.79, B:W.105, B:D.146, B:D.146 GOL.32: 10 residues within 4Å: Chain B: Q.86, G.90, I.92, S.116, D.117, F.118, V.383, E.384, R.387, E.463 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Q.86, B:S.116, B:E.384 Water bridges: B:E.384, B:R.387

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

NAG.5: 3 residues within 4Å: Chain A: N.52, T.54, L.55 Ligand excluded by PLIP NAG.6: 1 residues within 4Å: Chain A: N.125 Ligand excluded by PLIP NAG.7: 2 residues within 4Å: Chain A: I.240, N.242 Ligand excluded by PLIP NAG.8: 2 residues within 4Å: Chain A: N.319, S.321 Ligand excluded by PLIP NAG.9: 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.10: 4 residues within 4Å: Chain A: P.429, F.435, N.444, G.448 Ligand excluded by PLIP NAG.11: 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.12: 3 residues within 4Å: Chain A: M.481, N.483, S.485 Ligand excluded by PLIP NAG.13: 6 residues within 4Å: Chain A: E.293, D.534, S.537, N.539, L.559, K.561 Ligand excluded by PLIP NAG.14: 3 residues within 4Å: Chain A: T.545, K.551, N.555 Ligand excluded by PLIP NAG.15: 5 residues within 4Å: Chain A: N.58, A.59, T.60, N.644, S.646 Ligand excluded by PLIP NAG.21: 3 residues within 4Å: Chain B: N.52, T.54, L.55 Ligand excluded by PLIP NAG.22: 1 residues within 4Å: Chain B: N.125 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain B: I.240, N.242 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain B: N.319, S.321 Ligand excluded by PLIP NAG.25: 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.26: 4 residues within 4Å: Chain B: P.429, F.435, N.444, G.448 Ligand excluded by PLIP NAG.27: 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.28: 3 residues within 4Å: Chain B: M.481, N.483, S.485 Ligand excluded by PLIP NAG.29: 6 residues within 4Å: Chain B: E.293, D.534, S.537, N.539, L.559, K.561 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain B: T.545, K.551, N.555 Ligand excluded by PLIP NAG.31: 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., Structural Analysis of Beta-Fructofuranosidase from Xanthophyllomyces Dendrorhous Reveals Unique Features and the Crucial Role of N-Glycosylation in Oligomerization and Activity. J.Biol.Chem. (2016)

Release Date

2016-02-10

Peptides

BETA-FRUCTOFURANOSIDASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
B

BETA-FRUCTOFURANOSIDASE

Related Entries With Identical Sequence