SMTL ID : 6x5s.1

Human Alpha-1,6-fucosyltransferase (FUT8) bound to GDP and A3'-Asn

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.30 Å

Oligo State

homo-dimer

Ligands

2 x ASN: A3'-Asn(Non-covalent)

ASN.1: 2 residues within 4Å: Chain A: G.110 Ligands: NAG-NAG-BMA-MAN-NAG-NAG-MAN-NAG.2 Protein-ligand interaction information (PLIP) not available ASN.11: 4 residues within 4Å: Chain B: G.110, E.266 Ligands: NAG-NAG-BMA-MAN-NAG-NAG-MAN-NAG.12, GOL.19 Protein-ligand interaction information (PLIP) not available

2 x NAG- NAG- BMA- MAN- NAG- NAG- MAN- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]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-NAG-MAN-NAG.2: 27 residues within 4Å: Chain A: K.109, C.111, C.115, I.186, V.187, D.188, R.193, T.265, E.266, S.361, Q.363, D.387, D.388, I.389, Y.390, Y.391, G.393, G.394, Q.395, A.397, V.424, A.425, G.426, N.427, H.428, K.434 Ligands: ASN.1 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Y.390, A:Q.395, A:R.193, A:R.193, A:G.394, A:Q.395, A:Q.395 Water bridges: A:R.438 NAG-NAG-BMA-MAN-NAG-NAG-MAN-NAG.12: 26 residues within 4Å: Chain B: K.109, G.110, C.111, C.115, V.187, D.188, R.193, K.262, T.265, E.266, S.361, Q.363, D.387, D.388, Y.391, G.393, G.394, Q.395, V.424, A.425, G.426, N.427, H.428, K.434 Ligands: ASN.11, GOL.19 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.388, B:Q.395, B:V.424, B:R.193, B:R.193, B:G.394, B:Q.395

13 x CL: CHLORIDE ION(Non-functional Binders)

CL.3: 2 residues within 4Å: Chain A: R.452, K.454 Ligand excluded by PLIP CL.4: 2 residues within 4Å: Chain A: V.458, K.459 Ligand excluded by PLIP CL.5: 2 residues within 4Å: Chain A: K.249, H.250 Ligand excluded by PLIP CL.6: 2 residues within 4Å: Chain A: E.173, P.194 Ligand excluded by PLIP CL.7: 3 residues within 4Å: Chain A: Y.314, P.315, N.316 Ligand excluded by PLIP CL.8: 3 residues within 4Å: Chain A: P.94, K.95, D.96 Ligand excluded by PLIP CL.9: 2 residues within 4Å: Chain A: R.211 Chain B: K.3 Ligand excluded by PLIP CL.13: 2 residues within 4Å: Chain B: E.173, P.194 Ligand excluded by PLIP CL.14: 2 residues within 4Å: Chain B: P.233, W.234 Ligand excluded by PLIP CL.15: 2 residues within 4Å: Chain B: K.249, H.250 Ligand excluded by PLIP CL.16: 1 residues within 4Å: Chain B: R.208 Ligand excluded by PLIP CL.17: 1 residues within 4Å: Chain B: R.142 Ligand excluded by PLIP CL.18: 1 residues within 4Å: Chain B: K.95 Ligand excluded by PLIP

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

GDP.10: 21 residues within 4Å: Chain A: G.112, Y.113, G.114, C.115, Y.143, H.256, R.258, K.262, A.300, T.301, D.302, I.325, A.329, R.334, G.342, V.343, D.346, S.361, S.362, Q.363, V.364 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:G.112, A:Y.113, A:G.114, A:C.115, A:Y.143, A:H.256, A:G.342, A:Q.363, A:V.364 Salt bridges: A:R.258, A:K.262, A:D.346 GDP.20: 22 residues within 4Å: Chain B: G.112, Y.113, G.114, C.115, Y.143, H.256, R.258, K.262, A.300, T.301, D.302, I.325, A.329, R.334, G.342, V.343, D.346, S.361, S.362, Q.363, V.364 Ligands: GOL.19 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:G.112, B:Y.113, B:G.114, B:C.115, B:Y.143, B:Y.143, B:G.342, B:D.346, B:Q.363, B:V.364 Salt bridges: B:R.258, B:K.262, B:D.346

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.19: 8 residues within 4Å: Chain B: C.111, G.112, R.258, D.261, E.266 Ligands: ASN.11, NAG-NAG-BMA-MAN-NAG-NAG-MAN-NAG.12, GDP.20 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.112, B:R.258, B:D.261, B:E.266

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Boruah, B.M. et al., Characterizing human alpha-1,6-fucosyltransferase (FUT8) substrate specificity and structural similarities with related fucosyltransferases. J.Biol.Chem. (2020)

Release Date

2020-10-07

Peptides

Alpha-(1,6)-fucosyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Alpha-(1,6)-fucosyltransferase