Research workbench
The structure of arabidopsis thaliana FUT1 mutant R284K in complex with GDP
Analyse The structure of arabidopsis thaliana FUT1 mutant R284K in complex with GDP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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