Research workbench
Human alpha-1,6-fucosyltransferase (FUT8) bound to GDP and NM5M2-asn
Analyse Human alpha-1,6-fucosyltransferase (FUT8) bound to GDP and NM5M2-asn in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6X5U
- Type
- protein
- Length
- 3,736 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-(1,6)-fucosyltransferase
- EC
- 2.4.1.68
- UniProt
- Q9BYC5
- Ligands
- GDP, ASN, NAG, MAN, BMA
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 44% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | Alpha-(1,6)-fucosyltransferase (EC 2.4.1.68) | protein | 467 | 44% helix, 17% strand | Q9BYC5 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- ASN · Asparagine · ligand · 2 copies · chains A, G, C, H
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 20 copies · chains A, G, B, E, C, H, D, F
- MAN · alpha-D-mannopyranose · sugar · 14 copies · chains A, B, E, C, D, F, G, H
- BMA · beta-D-mannopyranose · sugar · 8 copies · chains A, B, E, C, D, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1053 | 0.85 | 0.86 | 81 | empty |
| 2 | 1045 | 0.85 | 0.86 | 80 | empty |
| 3 | 1142 | 0.84 | 0.85 | 87 | empty |
| 4 | 1139 | 0.84 | 0.85 | 131 | NAG, BMA, MAN, GDP |
| 5 | 1153 | 0.84 | 0.84 | 95 | empty |
Interfaces
12 interfaces between chains.
- A–B · 3341 Ų buried · 28 hydrogen bonds · protein-protein
- C–D · 3283 Ų buried · 24 hydrogen bonds · protein-protein
- B–E · 812 Ų buried · 3 hydrogen bonds · protein-protein
- F–H · 639 Ų buried · 7 hydrogen bonds · protein-protein
- A–F · 359 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 32 disulfide (disulfide).
Compared structures
- 6X5U · Human Alpha-1,6-fucosyltransferase (FUT8) bound to GDP and NM5M2-Asn · the same entry in another collection · chain G against G, TM-score 1.00
- Q9BYC5 · AlphaFold monomer V2.0 prediction for alpha-(1,6)-fucosyltransferase (Q9BYC5) · a predicted model of the same protein · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q9BYC5
- Elsewhere: RCSB PDB 6X5U · PDBe 6X5U · UniProt Q9BYC5
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