MolNFT v1 · #125043 · protein
The structure of arabidopsis thaliana FUT1 mutant R284K in complex with GDP
5KX6 · Galactoside 2-alpha-L-fucosyltransferase: “The structure of arabidopsis thaliana FUT1 mutant R284K in complex with GDP”. X-ray diffraction, 1 ligand (GDP), 11 pockets (best druggability 0.72). MolNFT v1 #125043 on GenesisL1: 3D…
- PDB
- 5KX6
- Type
- protein
- Length
- 890 residues
- Chains
- 2
- 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
- Pockets
- 11 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Galactoside 2-alpha-L-fucosyltransferase (EC 2.4.1.69) | protein | 440 | 38% helix, 16% strand | Q9SWH5 |
| B | Galactoside 2-alpha-L-fucosyltransferase (EC 2.4.1.69) | protein | 450 | 37% helix, 15% strand | Q9SWH5 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains A, B
- GOL · Glycerol · additive · chains B
- EDO · 1,2-ethanediol · additive · chains B
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 136 | 0.72 | 0.92 | 30 | empty |
| 2 | 82 | 0.60 | 0.89 | 22 | empty |
| 3 | 81 | 0.59 | 0.88 | 19 | empty |
| 4 | 60 | 0.56 | 0.89 | 19 | GOL |
| 5 | 247 | 0.56 | 0.78 | 43 | empty |
Interfaces
1 interface between chains.
- A–B · 458 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 5KX6 · The structure of Arabidopsis thaliana FUT1 Mutant R284K in complex with GDP · the same entry in another collection · chain A against A, 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 B 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 5KX6 · PDBe 5KX6 · UniProt Q9SWH5
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