Research workbench
Crystal structure of human alpha 1,6-fucosyltransferase, FUT8 bound to GDP and A2SGP
Analyse Crystal structure of human alpha 1,6-fucosyltransferase, FUT8 bound to GDP and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6VLD
- Type
- protein
- Length
- 1,854 residues
- Chains
- 4
- 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
- ASN, GDP, NAG, MAN, BMA, SO4
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 45% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alpha-(1,6)-fucosyltransferase (EC 2.4.1.68) | protein | 467 | 45% helix, 16% strand | Q9BYC5 |
| B | Alpha-(1,6)-fucosyltransferase (EC 2.4.1.68) | protein | 469 | 45% helix, 16% strand | Q9BYC5 |
| G | Alpha-(1,6)-fucosyltransferase (EC 2.4.1.68) | protein | 465 | 43% helix, 16% strand | Q9BYC5 |
| H | Alpha-(1,6)-fucosyltransferase (EC 2.4.1.68) | protein | 453 | 45% helix, 17% strand | Q9BYC5 |
Ligands and binding sites
- ASN · Asparagine · ligand · 4 copies · chains A, B, G, H
- GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 16 copies · chains A, B, G, H
- MAN · alpha-D-mannopyranose · sugar · 8 copies · chains A, B, G, H
- BMA · beta-D-mannopyranose · sugar · 4 copies · chains A, B, G, H
- SO4 · Sulfate ion · ion · 12 copies · chains A, B, 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, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 932 | 0.86 | 0.88 | 85 | empty |
| 2 | 962 | 0.85 | 0.86 | 84 | empty |
| 3 | 965 | 0.85 | 0.86 | 82 | empty |
| 4 | 1134 | 0.83 | 0.84 | 97 | empty |
| 5 | 208 | 0.70 | 0.87 | 38 | GDP |
Interfaces
3 interfaces between chains.
- B–G · 3460 Ų buried · 28 hydrogen bonds · protein-protein
- A–H · 3435 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 267 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 16 disulfide (disulfide).
Compared structures
- 6VLD · Crystal structure of human alpha 1,6-fucosyltransferase, FUT8 bound to GDP and A2SGP · the same entry in another collection · chain H against H, 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 6VLD · PDBe 6VLD · UniProt Q9BYC5
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