SMTL ID : 8d0q.1

Human FUT9 bound to GDP-CF3-Fucose and H-Type 2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.39 Å

Oligo State

homo-dimer

Ligands

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.1: 13 residues within 4Å: Chain A: R.88, P.90, F.91, Q.92, H.113, L.114, F.115, N.116, Y.310, K.311, S.312 Chain B: P.245, A.246 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:L.114 Hydrogen bonds: A:Y.310, B:A.246 Water bridges: B:D.247 NAG-NAG.8: 13 residues within 4Å: Chain A: P.245, A.246 Chain B: R.88, P.90, F.91, Q.92, H.113, L.114, F.115, N.116, Y.310, K.311, S.312 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:L.114 Hydrogen bonds: B:Y.310, A:A.246 Water bridges: A:D.247

2 x NAG- GAL- FUC: alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-GAL-FUC.2: 12 residues within 4Å: Chain A: F.36, Q.38, L.99, E.100, H.104, Y.131, N.209, F.292 Ligands: NDG-GAL-FUC.3, NDG-GAL-FUC.3, NDG-GAL-FUC.3, 6CK.4 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.100, A:Q.38, A:Q.38, A:Y.131, A:Y.131 Water bridges: A:F.36, A:Q.38, A:E.100 NAG-GAL-FUC.9: 12 residues within 4Å: Chain B: F.36, Q.38, L.99, E.100, H.104, Y.131, N.209, F.292 Ligands: NDG-GAL-FUC.10, NDG-GAL-FUC.10, NDG-GAL-FUC.10, 6CK.11 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.100, B:Q.38, B:Q.38, B:Y.131, B:Y.131 Water bridges: B:F.36, B:Q.38, B:E.100

2 x NDG- GAL- FUC: alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose

NDG-GAL-FUC.3: 12 residues within 4Å: Chain A: F.36, Q.38, L.99, E.100, H.104, Y.131, N.209, F.292 Ligands: NAG-GAL-FUC.2, NAG-GAL-FUC.2, NAG-GAL-FUC.2, 6CK.4 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.38, A:Q.38, A:Y.131, A:Y.131, A:E.100 Water bridges: A:E.100, A:F.36, A:Q.38 NDG-GAL-FUC.10: 12 residues within 4Å: Chain B: F.36, Q.38, L.99, E.100, H.104, Y.131, N.209, F.292 Ligands: NAG-GAL-FUC.9, NAG-GAL-FUC.9, NAG-GAL-FUC.9, 6CK.11 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.38, B:Q.38, B:Y.131, B:Y.131, B:E.100 Water bridges: B:E.100, B:F.36, B:Q.38

2 x 6CK: [(2R,3S,4R,5R)-5-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl (2R,3S,4R,5S,6R)-3,4,5-trihydroxy-6-(trifluoromethyl)tetrahydro-2H-pyran-2-yl dihydrogen diphosphate (non-preferred name)(Non-covalent)

6CK.4: 28 residues within 4Å: Chain A: E.100, Y.131, V.155, V.156, S.157, N.158, R.165, G.182, Q.183, Y.188, V.189, N.190, D.191, L.194, Y.204, N.209, Y.215, T.217, E.218, K.219, N.222 Ligands: NAG-GAL-FUC.2, NAG-GAL-FUC.2, NAG-GAL-FUC.2, NDG-GAL-FUC.3, NDG-GAL-FUC.3, NDG-GAL-FUC.3, GDP.5 23 PLIP interactions: 23 interactions with chain A Hydrogen bonds: A:Y.131, A:S.157, A:S.157, A:N.158, A:N.158, A:Q.183, A:V.189, A:V.189, A:Y.204, A:N.209, A:Y.215, A:E.218, A:E.218, A:N.222 Water bridges: A:E.100, A:S.101, A:D.191, A:D.191 Salt bridges: A:R.165, A:R.165, A:K.219, A:K.219, A:K.219 6CK.11: 28 residues within 4Å: Chain B: E.100, Y.131, V.155, V.156, S.157, N.158, R.165, G.182, Q.183, Y.188, V.189, N.190, D.191, L.194, Y.204, N.209, Y.215, T.217, E.218, K.219, N.222 Ligands: NAG-GAL-FUC.9, NAG-GAL-FUC.9, NAG-GAL-FUC.9, NDG-GAL-FUC.10, NDG-GAL-FUC.10, NDG-GAL-FUC.10, GDP.12 23 PLIP interactions: 23 interactions with chain B Hydrogen bonds: B:Y.131, B:S.157, B:S.157, B:N.158, B:N.158, B:Q.183, B:V.189, B:V.189, B:Y.204, B:N.209, B:Y.215, B:E.218, B:E.218, B:N.222 Water bridges: B:E.100, B:S.101, B:D.191, B:D.191 Salt bridges: B:R.165, B:R.165, B:K.219, B:K.219, B:K.219

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

GDP.5: 17 residues within 4Å: Chain A: V.155, V.156, S.157, N.158, R.165, G.182, Q.183, Y.188, V.189, N.190, D.191, L.194, Y.204, N.209, E.218, K.219 Ligands: 6CK.4 19 PLIP interactions: 19 interactions with chain A Hydrogen bonds: A:S.157, A:S.157, A:N.158, A:N.158, A:R.165, A:Q.183, A:V.189, A:V.189, A:N.190, A:Y.204, A:N.209, A:E.218 Water bridges: A:D.191, A:D.191, A:K.219, A:N.222, A:N.222 Salt bridges: A:R.165, A:K.219 GDP.12: 17 residues within 4Å: Chain B: V.155, V.156, S.157, N.158, R.165, G.182, Q.183, Y.188, V.189, N.190, D.191, L.194, Y.204, N.209, E.218, K.219 Ligands: 6CK.11 19 PLIP interactions: 19 interactions with chain B Hydrogen bonds: B:S.157, B:S.157, B:N.158, B:N.158, B:R.165, B:Q.183, B:V.189, B:V.189, B:N.190, B:Y.204, B:N.209, B:E.218 Water bridges: B:D.191, B:D.191, B:K.219, B:N.222, B:N.222 Salt bridges: B:R.165, B:K.219

4 x SO4: SULFATE ION(Non-functional Binders)

SO4.6: 6 residues within 4Å: Chain A: L.42, T.43, S.44, C.45, Q.46, C.54 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:C.45, A:Q.46, A:Q.46 Water bridges: A:A.47, A:C.54 SO4.7: 3 residues within 4Å: Chain A: P.290, R.291, F.292 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:P.290, A:F.292 Water bridges: A:R.291 Salt bridges: A:R.291 SO4.13: 6 residues within 4Å: Chain B: L.42, T.43, S.44, C.45, Q.46, C.54 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:C.45, B:Q.46, B:Q.46 Water bridges: B:A.47, B:C.54 SO4.14: 3 residues within 4Å: Chain B: P.290, R.291, F.292 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:P.290, B:F.292 Water bridges: B:R.291 Salt bridges: B:R.291

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kadirvelraj, R. et al., Structural basis for Lewis antigen synthesis by the alpha 1,3-fucosyltransferase FUT9. Nat.Chem.Biol. (2023)

Release Date

2023-05-31

Peptides

4-galactosyl-N-acetylglucosaminide 3-alpha-L-fucosyltransferase 9: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

4-galactosyl-N-acetylglucosaminide 3-alpha-L-fucosyltransferase 9

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