MolNFT v1 · #124762 · protein
Arabidopsis thaliana fucosyltransferase 1 (FUT1) in complex with GDP and a xylo-oligossacharide
5KOR · Galactoside 2-alpha-L-fucosyltransferase: “Arabidopsis thaliana fucosyltransferase 1 (FUT1) in complex with GDP and a xylo-oligossacharide”. X-ray diffraction, 5 ligands (GDP, BGC, XYS), 20 pockets (best druggability 0.77). MolNFT…
- PDB
- 5KOR
- Type
- protein
- Length
- 1,801 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Galactoside 2-alpha-L-fucosyltransferase
- EC
- 2.4.1.69
- UniProt
- Q9SWH5
- Ligands
- GDP, BGC, XYS, GAL, CL
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 39% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Galactoside 2-alpha-L-fucosyltransferase (EC 2.4.1.69) | protein | 450 | 40% helix, 15% strand | Q9SWH5 |
| B | Galactoside 2-alpha-L-fucosyltransferase (EC 2.4.1.69) | protein | 450 | 39% helix, 15% strand | Q9SWH5 |
| C | Galactoside 2-alpha-L-fucosyltransferase (EC 2.4.1.69) | protein | 449 | 39% helix, 15% strand | Q9SWH5 |
| D | Galactoside 2-alpha-L-fucosyltransferase (EC 2.4.1.69) | protein | 452 | 38% helix, 15% strand | Q9SWH5 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · 4 copies · chains A, B, C, D
- BGC · beta-D-glucopyranose · sugar · 8 copies · chains B, C
- XYS · alpha-D-xylopyranose · sugar · 6 copies · chains B, C
- GAL · beta-D-galactopyranose · sugar · 4 copies · chains B, C
- CL · Chloride ion · ion · 3 copies · chains B, C, D
- EDO · 1,2-ethanediol · additive · 14 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 108 | 0.77 | 0.97 | 29 | empty |
| 2 | 151 | 0.73 | 0.92 | 24 | EDO |
| 3 | 188 | 0.73 | 0.90 | 29 | EDO |
| 4 | 76 | 0.71 | 0.96 | 23 | EDO |
| 5 | 248 | 0.70 | 0.86 | 40 | GDP |
Interfaces
3 interfaces between chains.
- A–B · 1329 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 1315 Ų buried · 14 hydrogen bonds · protein-protein
- B–D · 372 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 20 disulfide (disulfide).
Compared structures
- 5KOR · Arabidopsis thaliana fucosyltransferase 1 (FUT1) in complex with GDP and a… · the same entry in another collection · chain D against D, TM-score 1.00
- Q9SWH5 · AlphaFold monomer V2.0 prediction for galactoside 2-alpha-L- fucosyltransferase (Q9SWH5) · a predicted model of the same protein · chain D 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 Q9SWH5
- Elsewhere: RCSB PDB 5KOR · PDBe 5KOR · UniProt Q9SWH5
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