SMTL ID : 8d0s.1

Human FUT9 bound to GDP and LNnT

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.37 Å

Oligo State

homo-dimer

Ligands

2 x NAG- NAG- BMA- MAN: 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

NAG-NAG-BMA-MAN.1: 16 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: R.237, P.245, A.246, D.247 Ligands: SO4.16 6 PLIP interactions: 2 interactions with chain B, 4 interactions with chain A Water bridges: B:E.241, B:R.237, B:R.237, B:A.246, B:D.247, A:R.88, A:H.113 Hydrogen bonds: B:A.246, A:Y.310 Hydrophobic interactions: A:L.114 NAG-NAG-BMA-MAN.11: 16 residues within 4Å: Chain A: R.237, P.245, A.246, D.247 Chain B: R.88, P.90, F.91, Q.92, H.113, L.114, F.115, N.116, Y.310, K.311, S.312 Ligands: SO4.6 6 PLIP interactions: 2 interactions with chain A, 4 interactions with chain B Water bridges: A:E.241, A:R.237, A:R.237, A:A.246, A:D.247, B:R.88, B:H.113 Hydrogen bonds: A:A.246, B:Y.310 Hydrophobic interactions: B:L.114

2 x GAL- NAG- GAL: beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-beta-D-galactopyranose

GAL-NAG-GAL.2: 9 residues within 4Å: Chain A: F.36, Q.38, L.99, E.100, H.104, Y.131, N.209, F.292 Ligands: EDO.9 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.100, A:Q.38, A:Y.131, A:Y.131 Water bridges: A:E.100 GAL-NAG-GAL.12: 9 residues within 4Å: Chain B: F.36, Q.38, L.99, E.100, H.104, Y.131, N.209, F.292 Ligands: EDO.19 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.100, B:Q.38, B:Y.131, B:Y.131 Water bridges: B:E.100

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

GDP.3: 16 residues within 4Å: Chain A: V.155, V.156, S.157, N.158, R.165, G.182, Y.188, V.189, N.190, D.191, L.194, Y.204, N.209, E.218, K.219, N.222 22 PLIP interactions: 22 interactions with chain A Hydrogen bonds: A:S.157, A:S.157, A:N.158, A:N.158, A:Q.183, A:V.189, A:V.189, A:N.190, A:Y.204, A:Y.204, A:N.209, A:E.218, A:E.218, A:N.222 Water bridges: A:R.165, A:R.165, A:Y.188, A:D.191, A:Y.215 Salt bridges: A:R.165, A:R.165, A:K.219 GDP.13: 16 residues within 4Å: Chain B: V.155, V.156, S.157, N.158, R.165, G.182, Y.188, V.189, N.190, D.191, L.194, Y.204, N.209, E.218, K.219, N.222 22 PLIP interactions: 22 interactions with chain B Hydrogen bonds: B:S.157, B:S.157, B:N.158, B:N.158, B:Q.183, B:V.189, B:V.189, B:N.190, B:Y.204, B:Y.204, B:N.209, B:E.218, B:E.218, B:N.222 Water bridges: B:R.165, B:R.165, B:Y.188, B:D.191, B:Y.215 Salt bridges: B:R.165, B:R.165, B:K.219

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

SO4.4: 6 residues within 4Å: Chain A: L.42, T.43, S.44, C.45, Q.46, C.54 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:L.42, A:C.45, A:Q.46, A:Q.46 Water bridges: A:A.47, A:C.54 SO4.5: 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 SO4.6: 5 residues within 4Å: Chain A: D.247, L.274, S.277, Y.278 Ligands: NAG-NAG-BMA-MAN.11 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.277, A:S.277 SO4.7: 3 residues within 4Å: Chain A: M.48, F.49, R.291 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.291 SO4.14: 6 residues within 4Å: Chain B: L.42, T.43, S.44, C.45, Q.46, C.54 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:L.42, B:C.45, B:Q.46, B:Q.46 Water bridges: B:A.47, B:C.54 SO4.15: 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 SO4.16: 5 residues within 4Å: Chain B: D.247, L.274, S.277, Y.278 Ligands: NAG-NAG-BMA-MAN.1 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.277, B:S.277 SO4.17: 3 residues within 4Å: Chain B: M.48, F.49, R.291 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.291

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

EDO.8: 7 residues within 4Å: Chain A: W.32, R.60, T.81, N.82, L.83, P.84, Q.85 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.82, A:Q.85 Water bridges: A:Q.86 EDO.9: 7 residues within 4Å: Chain A: F.36, R.74, E.100, H.104, P.106 Ligands: GAL-NAG-GAL.2, GAL-NAG-GAL.2 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.74 EDO.10: 4 residues within 4Å: Chain A: L.225, V.287, N.288, L.289 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.289, A:L.289 EDO.18: 7 residues within 4Å: Chain B: W.32, R.60, T.81, N.82, L.83, P.84, Q.85 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.82, B:Q.85 Water bridges: B:Q.86 EDO.19: 7 residues within 4Å: Chain B: F.36, R.74, E.100, H.104, P.106 Ligands: GAL-NAG-GAL.12, GAL-NAG-GAL.12 1 PLIP interactions: 1 interactions with chain B Water bridges: B:R.74 EDO.20: 4 residues within 4Å: Chain B: L.225, V.287, N.288, L.289 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:L.289, B:L.289

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

2023-05-24

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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