SMTL ID : 6tkv.1

Crystal structure of the human FUT8 in complex with GDP and a biantennary complex N-glycan

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

hetero-1-1-mer

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: 24 residues within 4Å: Chain A: K.109, C.111, C.115, I.186, V.187, D.188, E.266, S.346, Q.348, D.372, D.373, I.374, Y.376, F.377, G.378, G.379, Q.380, A.382, V.409, A.410, G.411, N.412, H.413, K.419 3 PLIP interactions: 3 interactions with chain A Water bridges: A:D.373, A:I.374, A:Y.375, A:V.409 Hydrogen bonds: A:Q.380, A:G.379, A:Q.380, A:A.382 NAG-NAG-BMA-MAN-NAG-MAN-NAG.16: 26 residues within 4Å: Chain B: K.110, G.111, C.112, C.116, I.187, V.188, D.189, E.267, S.362, Q.364, D.388, D.389, I.390, Y.392, F.393, G.394, G.395, Q.396, A.398, V.425, A.426, G.427, N.428, H.429, K.435 Ligands: GOL.18 3 PLIP interactions: 3 interactions with chain B Water bridges: B:D.389, B:I.390, B:Y.391, B:V.425, B:H.399 Hydrogen bonds: B:Q.396, B:G.395, B:Q.396

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

GDP.2: 18 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, G.327, V.328, D.331, S.346, S.347, Q.348, V.349 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:G.112, A:Y.113, A:G.114, A:C.115, A:Y.143, A:Y.143, A:R.258, A:G.327, A:D.331, A:S.346, A:Q.348, A:V.349 Water bridges: A:K.262 Salt bridges: A:R.258, A:K.262, A:D.331 GDP.17: 22 residues within 4Å: Chain B: G.113, Y.114, G.115, C.116, Y.144, H.257, R.259, K.263, A.301, T.302, D.303, I.326, A.330, R.335, G.343, V.344, D.347, S.362, S.363, Q.364, V.365 Ligands: GOL.18 16 PLIP interactions: 16 interactions with chain B Hydrogen bonds: B:G.113, B:Y.114, B:G.115, B:C.116, B:Y.144, B:G.343, B:S.362, B:Q.364, B:V.365 Water bridges: B:R.335, B:R.335, B:V.344, B:V.344 Salt bridges: B:R.259, B:K.263, B:D.347

17 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 8 residues within 4Å: Chain A: F.22, E.26, H.41, E.44, F.45, D.48 Chain B: R.410, Y.433 Ligand excluded by PLIP GOL.4: 7 residues within 4Å: Chain A: H.278, E.281, H.282, F.340, H.369 Chain B: F.22 Ligands: GOL.10 Ligand excluded by PLIP GOL.5: 5 residues within 4Å: Chain A: E.274, H.278, H.369, L.371, W.414 Ligand excluded by PLIP GOL.6: 5 residues within 4Å: Chain A: C.97, T.158, C.159, T.160, D.161 Ligand excluded by PLIP GOL.7: 5 residues within 4Å: Chain A: K.99, K.101, I.165, N.178, Q.180 Ligand excluded by PLIP GOL.8: 6 residues within 4Å: Chain A: L.91, P.94, A.100, K.101, Q.131, T.133 Ligand excluded by PLIP GOL.9: 4 residues within 4Å: Chain A: H.250, Q.337, L.360, H.361 Ligand excluded by PLIP GOL.10: 7 residues within 4Å: Chain A: A.366, F.368, H.369, W.414 Chain B: K.18, F.22 Ligands: GOL.4 Ligand excluded by PLIP GOL.11: 6 residues within 4Å: Chain A: I.386, A.387, I.388, P.403, G.404, R.437 Ligand excluded by PLIP GOL.12: 4 residues within 4Å: Chain A: R.437, E.438, I.440 Chain B: I.8 Ligand excluded by PLIP GOL.13: 6 residues within 4Å: Chain A: K.17, F.21 Chain B: A.382, F.384, H.385, W.430 Ligand excluded by PLIP GOL.14: 6 residues within 4Å: Chain A: V.104, N.106, E.137, E.183, L.184, P.185 Ligand excluded by PLIP GOL.15: 2 residues within 4Å: Chain A: R.11, Y.62 Ligand excluded by PLIP GOL.18: 7 residues within 4Å: Chain B: G.113, R.259, D.262, E.267, R.335 Ligands: NAG-NAG-BMA-MAN-NAG-MAN-NAG.16, GDP.17 Ligand excluded by PLIP GOL.19: 4 residues within 4Å: Chain B: G.3, K.4, D.5, D.68 Ligand excluded by PLIP GOL.20: 4 residues within 4Å: Chain B: F.153, I.230, I.240, H.349 Ligand excluded by PLIP GOL.21: 7 residues within 4Å: Chain A: R.394 Chain B: F.23, E.27, H.42, E.45, F.46, D.49 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Garcia-Garcia, A. et al., Structural basis for substrate specificity and catalysis of alpha 1,6-fucosyltransferase. Nat Commun (2020)

Release Date

2020-01-29

Peptides

Alpha-(1,6)-fucosyltransferase: A
Alpha-(1,6)-fucosyltransferase: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
A

Alpha-(1,6)-fucosyltransferase

Alpha-(1,6)-fucosyltransferase