SMTL ID : 8d0r.1

Human FUT9 bound to GDP and H-Type 2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.40 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: 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: 3 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:L.114 Hydrogen bonds: A:Y.310, B:A.246 Water bridges: A:H.113, B:E.241 NAG-NAG-BMA.10: 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: 3 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:L.114 Hydrogen bonds: B:Y.310, A:A.246 Water bridges: B:H.113, A:E.241

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: 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:Q.38, A:Q.38, A:E.100 Water bridges: A:E.100, A:F.36, A:Q.38, A:N.209 NAG-GAL-FUC.11: 9 residues within 4Å: Chain B: F.36, Q.38, L.99, E.100, H.104, Y.131, N.209, F.292 Ligands: EDO.18 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.38, B:Q.38, B:E.100 Water bridges: B:E.100, B:F.36, B:Q.38, B:N.209

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

GDP.3: 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, N.222 20 PLIP interactions: 20 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:D.191, A:D.191 Salt bridges: A:R.165, A:R.165, A:K.219, 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, N.222 20 PLIP interactions: 20 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:D.191, B:D.191 Salt bridges: B:R.165, B:R.165, B:K.219, B:K.219

6 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 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 SO4.5: 3 residues within 4Å: Chain A: P.290, R.291, F.292 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:P.290, A:F.292 Salt bridges: A:R.291 SO4.6: 3 residues within 4Å: Chain A: W.159, A.184, F.185 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:W.159, A:A.184 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 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:P.290, B:F.292 Salt bridges: B:R.291 SO4.15: 3 residues within 4Å: Chain B: W.159, A.184, F.185 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:W.159, B:A.184

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

EDO.7: 3 residues within 4Å: Chain A: D.247, S.277, Y.278 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.247, A:S.277 EDO.8: 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.9: 6 residues within 4Å: Chain A: F.36, R.74, E.100, H.104, P.106 Ligands: NAG-GAL-FUC.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.104 EDO.16: 3 residues within 4Å: Chain B: D.247, S.277, Y.278 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.247, B:S.277 EDO.17: 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 EDO.18: 6 residues within 4Å: Chain B: F.36, R.74, E.100, H.104, P.106 Ligands: NAG-GAL-FUC.11 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.104

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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