MolNFT v1 · #165130 · protein
Crystal structure of the human FUT8 in complex with GDP and a biantennary complex N-glycan
6TKV · Alpha-(1,6)-fucosyltransferase: “Crystal structure of the human FUT8 in complex with GDP and a biantennary complex N-glycan”. X-ray diffraction, 4 ligands (GDP, NAG, MAN), 8 pockets (best druggability 0.70). MolNFT v1 #165130 on…
- PDB
- 6TKV
- Type
- protein
- Length
- 921 residues
- Chains
- 2
- 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, NAG, MAN, BMA
- Pockets
- 8 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alpha-(1,6)-fucosyltransferase (EC 2.4.1.68) | protein | 468 | 46% helix, 17% strand | Q9BYC5 |
| B | Alpha-(1,6)-fucosyltransferase (EC 2.4.1.68) | protein | 453 | 45% helix, 17% strand | Q9BYC5 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · 4 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 2 copies · chains A, B
- GOL · Glycerol · additive · 17 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 820 | 0.70 | 0.76 | 76 | GOL |
| 2 | 197 | 0.69 | 0.87 | 30 | GDP, GOL |
| 3 | 453 | 0.63 | 0.77 | 43 | empty |
| 4 | 190 | 0.60 | 0.82 | 29 | GOL |
| 5 | 199 | 0.59 | 0.81 | 36 | empty |
Interfaces
1 interface between chains.
- A–B · 474 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 6TKV · Crystal structure of the human FUT8 in complex with GDP and a biantennary complex N-glycan · the same entry in another collection · chain A against A, 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 6TKV · PDBe 6TKV · UniProt Q9BYC5
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