SMTL ID : 6vld.1 (1 other biounit)

Crystal structure of human alpha 1,6-fucosyltransferase, FUT8 bound to GDP and A2SGP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.28 Å

Oligo State

homo-dimer

Ligands

2 x NAG- NAG- BMA- MAN- NAG- MAN- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]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-NAG-MAN-NAG.1: 29 residues within 4Å: Chain A: K.112, C.114, C.118, I.189, V.190, D.191, R.196, K.265, T.268, E.269, Q.366, D.390, D.391, I.392, Y.394, F.395, G.396, G.397, Q.398, A.400, V.427, A.428, G.429, N.430, H.431, K.437, R.441 Ligands: ASN.3, SO4.8 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.391, A:Q.398, A:R.196, A:R.196, A:G.397, A:Q.398, A:R.441 Water bridges: A:D.391, A:Y.393, A:H.401 NAG-NAG-BMA-MAN-NAG-MAN-NAG.2: 27 residues within 4Å: Chain B: K.112, G.113, C.114, C.118, I.189, V.190, D.191, R.196, Q.366, D.390, D.391, I.392, Y.394, F.395, G.396, G.397, Q.398, A.400, V.427, A.428, G.429, N.430, H.431, K.437 Ligands: ASN.9, SO4.11, SO4.14 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:Q.398, B:R.196, B:R.196, B:G.397, B:Q.398 Water bridges: B:Y.393, B:H.401, B:R.441

2 x ASN: ASPARAGINE(Non-covalent)

ASN.3: 2 residues within 4Å: Chain A: G.113 Ligands: NAG-NAG-BMA-MAN-NAG-MAN-NAG.1 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Ligand interactions Hydrogen bonds: A:G.113, N.3, N.3 ASN.9: 2 residues within 4Å: Chain B: G.113 Ligands: NAG-NAG-BMA-MAN-NAG-MAN-NAG.2 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Ligand interactions Hydrogen bonds: B:G.113, N.9, N.9

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

GDP.4: 20 residues within 4Å: Chain A: G.115, Y.116, G.117, C.118, Y.146, H.259, R.261, K.265, A.303, T.304, D.305, I.328, A.332, R.337, G.345, V.346, D.349, S.365, Q.366, V.367 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:G.115, A:Y.116, A:G.117, A:C.118, A:Y.146, A:G.345, A:D.349, A:S.364, A:Q.366, A:V.367 Water bridges: A:T.304, A:T.304, A:R.337, A:R.337 Salt bridges: A:R.261, A:K.265, A:D.349

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

SO4.5: 4 residues within 4Å: Chain A: L.193, H.194, P.195, R.196 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.196 SO4.6: 2 residues within 4Å: Chain A: K.252, H.253 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.253, A:H.253 Salt bridges: A:H.253 SO4.7: 1 residues within 4Å: Chain A: Q.142 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.142, A:R.165 SO4.8: 3 residues within 4Å: Chain A: H.431, K.437 Ligands: NAG-NAG-BMA-MAN-NAG-MAN-NAG.1 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:H.431, A:K.437 SO4.10: 3 residues within 4Å: Chain B: N.109, N.111, N.143 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.109, B:N.111, B:N.143 SO4.11: 4 residues within 4Å: Chain B: R.261, S.365, Q.366 Ligands: NAG-NAG-BMA-MAN-NAG-MAN-NAG.2 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.366 Water bridges: B:R.261, B:R.369 Salt bridges: B:R.261 SO4.12: 4 residues within 4Å: Chain B: L.193, H.194, P.195, R.196 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.196 Salt bridges: B:H.194 SO4.13: 3 residues within 4Å: Chain B: F.251, K.252, H.253 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:H.253 Salt bridges: B:H.253 SO4.14: 3 residues within 4Å: Chain B: H.431, K.437 Ligands: NAG-NAG-BMA-MAN-NAG-MAN-NAG.2 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:H.431, B:K.437

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jarva, M.A. et al., Structural basis of substrate recognition and catalysis by fucosyltransferase 8. J.Biol.Chem. (2020)

Release Date

2020-02-26

Peptides

Alpha-(1,6)-fucosyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
H

Alpha-(1,6)-fucosyltransferase

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