SMTL ID : 6x5r.1

Human Alpha-1,6-fucosyltransferase (FUT8) bound to GDP and A2-Asn

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-dimer

Ligands

2 x ASN: A2-Asn(Non-covalent)

ASN.1: 3 residues within 4Å: Chain A: G.177, E.333 Ligands: NAG-NAG-BMA-MAN-NAG-MAN-NAG.2 Protein-ligand interaction information (PLIP) not available ASN.8: 2 residues within 4Å: Chain B: G.177 Ligands: NAG-NAG-BMA-MAN-NAG-MAN-NAG.9 Protein-ligand interaction information (PLIP) not available

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.2: 30 residues within 4Å: Chain A: K.176, G.177, C.178, C.182, I.253, V.254, D.255, R.260, K.329, T.332, E.333, S.428, Q.430, D.454, D.455, I.456, Y.458, F.459, G.460, G.461, Q.462, A.464, V.491, A.492, G.493, N.494, H.495, K.501 Ligands: ASN.1, GOL.4 4 PLIP interactions: 4 interactions with chain A Water bridges: A:A.492, A:Y.457, A:H.465 Hydrogen bonds: A:Q.462, A:R.260, A:G.461, A:Q.462 NAG-NAG-BMA-MAN-NAG-MAN-NAG.9: 26 residues within 4Å: Chain B: K.176, C.178, C.182, I.253, V.254, D.255, R.260, K.329, E.333, S.428, Q.430, D.454, D.455, Y.458, F.459, G.460, G.461, Q.462, A.464, V.491, A.492, G.493, N.494, H.495, K.501 Ligands: ASN.8 7 PLIP interactions: 7 interactions with chain B Water bridges: B:A.492, B:I.456, B:Y.457, B:V.491, B:G.461, B:H.465, B:R.505 Hydrogen bonds: B:Q.462, B:R.260, B:R.260, B:G.461, B:Q.462

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

EDO.3: 4 residues within 4Å: Chain A: L.203, E.204, S.205, Q.206 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.205, A:Q.206, A:Q.206 Water bridges: A:S.205, A:E.216 EDO.5: 3 residues within 4Å: Chain A: P.161, K.162, D.163 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.162, A:D.163, A:D.163 EDO.10: 5 residues within 4Å: Chain B: Q.198, P.528, T.529, Y.530, P.531 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.529, B:Y.530 EDO.11: 2 residues within 4Å: Chain B: H.118, Q.351 No protein-ligand interaction detected (PLIP)

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 8 residues within 4Å: Chain A: C.178, G.179, C.182, R.325, D.328, E.333 Ligands: NAG-NAG-BMA-MAN-NAG-MAN-NAG.2, GDP.7 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.179, A:R.325, A:D.328, A:E.333 Water bridges: A:Y.402

2 x MN: MANGANESE (II) ION(Non-covalent)

MN.6: 3 residues within 4Å: Chain A: E.348, H.349, H.451 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.349, A:H.451, H2O.2 MN.12: 3 residues within 4Å: Chain B: E.348, H.349, H.451 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.349, B:H.451, H2O.14

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

GDP.7: 22 residues within 4Å: Chain A: G.179, Y.180, G.181, C.182, Y.210, H.323, R.325, K.329, A.367, T.368, D.369, I.392, A.396, R.401, G.409, V.410, D.413, S.428, S.429, Q.430, V.431 Ligands: GOL.4 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:G.179, A:Y.180, A:G.181, A:C.182, A:Y.210, A:G.409, A:Q.430, A:V.431 Water bridges: A:R.401, A:R.401, A:V.410, A:V.410 Salt bridges: A:R.325, A:K.329, A:D.413 GDP.13: 21 residues within 4Å: Chain B: G.179, Y.180, G.181, C.182, Y.210, H.323, R.325, K.329, A.367, T.368, D.369, I.392, A.396, R.401, G.409, V.410, D.413, S.428, S.429, Q.430, V.431 20 PLIP interactions: 20 interactions with chain B Hydrogen bonds: B:G.179, B:Y.180, B:G.181, B:C.182, B:Y.210, B:Y.210, B:G.409, B:D.413, B:Q.430, B:V.431 Water bridges: B:R.325, B:T.368, B:T.368, B:R.401, B:R.401, B:V.410, B:V.410 Salt bridges: B:R.325, B:K.329, B:D.413

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
B

B
A

Alpha-(1,6)-fucosyltransferase

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