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

Arabidopsis thaliana fucosyltransferase 1 (FUT1) in complex with GDP and a xylo-oligossacharide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-dimer

Ligands

1 x BGC- BGC- BGC- BGC- XYS- XYS- GAL- XYS- GAL: alpha-D-xylopyranose-(1-6)-beta-D-glucopyranose-(1-4)-[beta-D-galactopyranose-(1-2)-alpha-D-xylopyranose-(1-6)]beta-D-glucopyranose-(1-4)-[beta-D-galactopyranose-(1-2)-alpha-D-xylopyranose-(1-6)]beta-D-glucopyranose-(1-4)-beta-D-glucopyranose

BGC-BGC-BGC-BGC-XYS-XYS-GAL-XYS-GAL.1: 14 residues within 4Å: Chain A: N.147, H.234, K.241, N.264, F.331, D.332, W.444, T.446, R.464, H.486, S.487, P.488, F.490, W.516 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.147, A:N.147, A:N.264, A:H.486, A:S.487 Water bridges: A:W.444

2 x GDP: GUANOSINE-5'-DIPHOSPHATE(Non-covalent)

GDP.2: 18 residues within 4Å: Chain A: G.144, L.145, G.146, N.147, R.329, F.331, T.379, S.380, L.381, S.410, E.412, H.422, A.426, E.429, W.444, S.445, T.446, F.447 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:L.145, A:G.146, A:N.147, A:T.379, A:S.410, A:S.410, A:N.423, A:W.444, A:T.446, A:T.446, A:F.447 Water bridges: A:G.144, A:Q.327, A:L.381 Salt bridges: A:R.329, A:E.429 pi-Stacking: A:F.447 GDP.10: 18 residues within 4Å: Chain B: G.144, L.145, G.146, N.147, R.329, F.331, T.379, S.380, L.381, S.410, Q.415, H.422, A.426, E.429, W.444, S.445, T.446, F.447 21 PLIP interactions: 21 interactions with chain B Hydrogen bonds: B:L.145, B:G.146, B:N.147, B:S.410, B:S.410, B:W.444, B:T.446, B:T.446, B:F.447 Water bridges: B:G.144, B:Q.327, B:S.380, B:L.381, B:L.381, B:Q.415, B:T.417, B:E.429 Salt bridges: B:R.329, B:E.429 pi-Stacking: B:F.447, B:F.447

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

EDO.3: 6 residues within 4Å: Chain A: R.329, V.341, Q.344, S.442, L.462, P.465 2 PLIP interactions: 2 interactions with chain A Water bridges: A:F.331, A:A.443 EDO.4: 4 residues within 4Å: Chain A: H.82, Y.83, Y.313, E.314 No protein-ligand interaction detected (PLIP) EDO.5: 9 residues within 4Å: Chain A: Q.204, C.209, G.211, Y.212, K.215, G.237, D.238, H.239, D.240 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.211, A:K.215, A:G.237, A:H.239 Water bridges: A:D.238 EDO.6: 6 residues within 4Å: Chain A: H.373, A.375, I.403, G.405, H.407 Chain B: A.315 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.373, A:H.407 EDO.7: 5 residues within 4Å: Chain A: Y.89, Q.286, K.287, A.288, M.481 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.288 Water bridges: A:P.285, A:K.287 EDO.8: 2 residues within 4Å: Chain A: D.334 Ligands: CL.9 No protein-ligand interaction detected (PLIP) EDO.11: 7 residues within 4Å: Chain B: R.329, V.341, Q.344, S.442, L.462, Y.463, P.465 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.344 Water bridges: B:R.329, B:A.443 EDO.12: 6 residues within 4Å: Chain A: E.387, K.390 Chain B: Q.408, P.409, S.410, Q.411 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:P.409, A:K.390 Water bridges: B:Q.408 EDO.13: 7 residues within 4Å: Chain A: A.383, Q.408, P.409, S.410, Q.411 Chain B: E.387, K.390 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:P.409, B:K.390 Water bridges: A:E.387, A:E.387, A:Q.408

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

CL.9: 2 residues within 4Å: Chain A: Q.339 Ligands: EDO.8 Ligand excluded by PLIP CL.14: 1 residues within 4Å: Chain B: Q.339 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rocha, J. et al., Structure of Arabidopsis thaliana FUT1 Reveals a Variant of the GT-B Class Fold and Provides Insight into Xyloglucan Fucosylation. Plant Cell (2016)

Release Date

2016-10-12

Peptides

Galactoside 2-alpha-L-fucosyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

Galactoside 2-alpha-L-fucosyltransferase

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