SMTL ID : 8d0x.1

Human FUT9 bound to LNnT

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.33 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 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Water bridges: B:E.241, B:R.237, B:A.246, B:D.247, A:H.113 Hydrogen bonds: B:A.246 Hydrophobic interactions: A:L.114 NAG-NAG-BMA-MAN.12: 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: SO4.5 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Water bridges: A:E.241, A:R.237, B:H.113, A:A.246, A:D.247 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: GOL.11 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.100, A:Q.38, A:E.100, A:Y.131, A:Y.131 Water bridges: A:Q.38, A:E.100 GAL-NAG-GAL.13: 9 residues within 4Å: Chain B: F.36, Q.38, L.99, E.100, H.104, Y.131, N.209, F.292 Ligands: GOL.22 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.100, B:Q.38, B:Y.131 Water bridges: B:Q.38, B:E.100

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

SO4.3: 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:T.43, A:C.45, A:Q.46 Water bridges: A:A.47, A:C.54 SO4.4: 3 residues within 4Å: Chain A: P.290, R.291, F.292 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:F.292 Water bridges: A:R.291 Salt bridges: A:R.291 SO4.5: 5 residues within 4Å: Chain A: D.247, L.274, S.277, Y.278 Ligands: NAG-NAG-BMA-MAN.12 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.277, A:S.277 SO4.6: 3 residues within 4Å: Chain A: W.159, A.184, F.185 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.184 SO4.14: 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:T.43, B:C.45, 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 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: 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 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.277, B:S.277 Water bridges: B:D.247, B:D.247, B:Y.278 SO4.17: 3 residues within 4Å: Chain B: W.159, A.184, F.185 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:A.184

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

EDO.7: 3 residues within 4Å: Chain A: T.138, N.139, T.286 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.138, A:T.138, A:V.287 Water bridges: A:T.138, A:V.287 EDO.8: 4 residues within 4Å: Chain A: R.74, D.75, I.76, W.78 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.74, A:I.76 Water bridges: A:W.78, A:K.108 EDO.9: 1 residues within 4Å: Chain A: N.64 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.64, A:Q.86 Water bridges: A:S.61 EDO.10: 2 residues within 4Å: Chain A: H.212, K.213 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.212, A:K.213 EDO.18: 3 residues within 4Å: Chain B: T.138, N.139, T.286 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:T.138, B:T.286, B:V.287 Water bridges: B:T.138, B:V.287 EDO.19: 4 residues within 4Å: Chain B: R.74, D.75, I.76, W.78 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.74, B:I.76 Water bridges: B:W.78, B:K.108 EDO.20: 1 residues within 4Å: Chain B: N.64 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.64, B:Q.86 Water bridges: B:S.61 EDO.21: 2 residues within 4Å: Chain B: H.212, K.213 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:H.212, B:K.213

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.11: 8 residues within 4Å: Chain A: F.36, R.74, E.100, H.104, T.105, P.106 Ligands: GAL-NAG-GAL.2, GAL-NAG-GAL.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.104 Water bridges: A:R.74 GOL.22: 8 residues within 4Å: Chain B: F.36, R.74, E.100, H.104, T.105, P.106 Ligands: GAL-NAG-GAL.13, GAL-NAG-GAL.13 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:H.104 Water bridges: B:R.74

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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