Research workbench
Human alpha-1,6-fucosyltransferase (FUT8) bound to GDP
Analyse Human alpha-1,6-fucosyltransferase (FUT8) bound to GDP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6X5H
- Type
- protein
- Length
- 1,833 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
- GDP
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 3 distinct chains · 45% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Alpha-(1,6)-fucosyltransferase (EC 2.4.1.68) | protein | 467 | 46% helix, 17% strand | Q9BYC5 |
| C | Alpha-(1,6)-fucosyltransferase (EC 2.4.1.68) | protein | 449 | 45% helix, 17% strand | Q9BYC5 |
| D | Alpha-(1,6)-fucosyltransferase (EC 2.4.1.68) | protein | 450 | 44% helix, 17% strand | Q9BYC5 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · 3 copies · chains A, B, C
- EDO · 1,2-ethanediol · additive · 10 copies · chains A, B, C, D
- GOL · Glycerol · additive · 4 copies · chains A, B
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 | 998 | 0.86 | 0.87 | 84 | empty |
| 2 | 1139 | 0.84 | 0.84 | 97 | empty |
| 3 | 318 | 0.77 | 0.88 | 53 | empty |
| 4 | 169 | 0.70 | 0.89 | 28 | GDP |
| 5 | 183 | 0.70 | 0.88 | 32 | GDP |
Interfaces
3 interfaces between chains.
- B–C · 3363 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 800 Ų buried · 21 hydrogen bonds · protein-protein
- C–D · 181 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 16 disulfide (disulfide).
Compared structures
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 6X5H · PDBe 6X5H · UniProt Q9BYC5
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