SMTL ID : 8beq.1

Structure of fructofuranosidase from Rhodotorula dairenensis

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.07 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: 7 residues within 4Å: Chain A: S.307, A.328, D.331, T.333, E.335, F.347, N.350 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.331 NAG-NAG-BMA.4: 9 residues within 4Å: Chain A: P.598 Chain B: D.542, S.544, N.546, T.571, F.573, A.651, T.652, G.653 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.542

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.2: 9 residues within 4Å: Chain A: D.542, S.544, N.546, F.573, A.651, T.652, G.653 Chain B: N.597, P.598 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Water bridges: B:N.597 Hydrogen bonds: A:D.542 NAG-NAG.3: 6 residues within 4Å: Chain B: A.328, D.331, T.333, E.335, F.347, N.350 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:A.328 Hydrogen bonds: B:D.331

9 x MAN: alpha-D-mannopyranose(Post Translational Modification)

MAN.5: 3 residues within 4Å: Chain A: T.146, S.147 Ligands: MAN.6 No protein-ligand interaction detected (PLIP) MAN.6: 3 residues within 4Å: Chain A: S.147 Ligands: MAN.5, MAN.7 No protein-ligand interaction detected (PLIP) MAN.7: 5 residues within 4Å: Chain A: T.153, E.154, S.457, A.458 Ligands: MAN.6 No protein-ligand interaction detected (PLIP) MAN.17: 4 residues within 4Å: Chain B: T.146, S.147, S.557 Ligands: MAN.18 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.557 MAN.18: 3 residues within 4Å: Chain B: S.147, L.148 Ligands: MAN.17 1 PLIP interactions: 1 interactions with chain B Water bridges: B:L.148 MAN.19: 2 residues within 4Å: Chain B: P.149, S.151 No protein-ligand interaction detected (PLIP) MAN.20: 5 residues within 4Å: Chain B: A.150, T.153, E.154, S.457, A.458 No protein-ligand interaction detected (PLIP) MAN.21: 3 residues within 4Å: Chain B: V.159, T.161, F.237 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:V.159 MAN.22: 2 residues within 4Å: Chain B: T.161, T.163 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.161

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

NAG.8: 4 residues within 4Å: Chain A: N.240, T.242, L.274, T.276 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.242, A:T.242 NAG.9: 5 residues within 4Å: Chain A: Y.297, P.340, N.341, T.343, S.344 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.341, A:T.343, A:T.343, A:S.344 NAG.10: 4 residues within 4Å: Chain A: N.405, T.407, H.408, V.410 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:T.407 Hydrogen bonds: A:T.407 Water bridges: A:N.405 NAG.11: 5 residues within 4Å: Chain A: F.371, L.473, T.474, N.475, W.481 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.371, A:W.481 Hydrogen bonds: A:N.475 NAG.12: 6 residues within 4Å: Chain A: A.504, N.505, G.654, L.655, P.656, E.657 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:A.504 Hydrogen bonds: A:P.656 Water bridges: A:G.654, A:G.654 NAG.13: 5 residues within 4Å: Chain A: S.523, N.525, N.662, L.663, Q.664 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:N.662 Hydrogen bonds: A:S.523, A:S.523, A:N.525, A:N.662 NAG.23: 4 residues within 4Å: Chain B: D.195, N.197, D.266, G.290 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.197, B:D.266 NAG.24: 5 residues within 4Å: Chain B: P.239, N.240, T.242, L.274, T.276 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.240, B:T.242, B:T.242 NAG.25: 2 residues within 4Å: Chain B: P.262, N.263 No protein-ligand interaction detected (PLIP) NAG.26: 5 residues within 4Å: Chain B: Y.297, P.340, N.341, T.343, S.344 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.341, B:T.343, B:T.343 Water bridges: B:T.343 NAG.27: 4 residues within 4Å: Chain B: N.405, T.407, H.408, V.410 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:T.407 Hydrogen bonds: B:T.407 Water bridges: B:N.405 NAG.28: 5 residues within 4Å: Chain B: F.371, L.473, T.474, N.475, W.481 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:F.371, B:W.481 Hydrogen bonds: B:N.475 NAG.29: 7 residues within 4Å: Chain B: A.504, N.505, G.654, L.655, P.656, E.657, T.659 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:A.504 Hydrogen bonds: B:P.656, B:E.657, B:E.657 Water bridges: B:G.654 NAG.30: 5 residues within 4Å: Chain B: S.523, N.525, N.662, L.663, Q.664 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:Q.664 Hydrogen bonds: B:S.523, B:S.523, B:N.525

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

PEG.14: 10 residues within 4Å: Chain A: N.187, D.188, Q.205, Q.216, F.246, S.247, R.311, D.312, E.362, C.363 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.187, A:Q.216, A:E.362

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.15: 12 residues within 4Å: Chain A: V.164, I.165, Y.179, P.182, Y.204, Y.206, G.219, H.220, N.231, Q.232, P.233, I.234 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:T.163, A:I.165, A:H.220, A:H.220, A:N.231, A:Q.232 GOL.16: 2 residues within 4Å: Chain A: N.387, W.448 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:N.387 Water bridges: A:R.311, A:N.387, B:L.577 GOL.31: 9 residues within 4Å: Chain B: N.187, D.188, Q.205, Q.216, F.246, S.247, R.311, D.312 Ligands: BTB.32 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.187, B:D.188, B:Q.216, B:S.247, B:D.312 GOL.33: 13 residues within 4Å: Chain B: T.163, V.164, I.165, Y.179, P.182, Y.204, Y.206, G.219, H.220, N.231, Q.232, P.233, I.234 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:T.163, B:I.165, B:Y.179, B:Y.204, B:H.220, B:Q.232

1 x BTB: 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-covalent)

BTB.32: 5 residues within 4Å: Chain B: R.311, E.362, N.387, W.448 Ligands: GOL.31 7 PLIP interactions: 5 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:R.311, B:E.362, B:N.387 Water bridges: B:R.311, A:L.577, A:N.579 Salt bridges: B:E.362

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jimenez-Ortega, E. et al., Insights into the Structure of the Highly Glycosylated Ffase from Rhodotorula dairenensis Enhance Its Biotechnological Potential. Int J Mol Sci (2022)

Release Date

2022-12-28

Peptides

Fructofuranosidase from Rhodotorula dairenensis: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Fructofuranosidase from Rhodotorula dairenensis