Research workbench
Arabidopsis thaliana fucosyltransferase 1 (FUT1) in its apo-form
Analyse Arabidopsis thaliana fucosyltransferase 1 (FUT1) in its apo-form in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5KOP
- Type
- protein
- Length
- 1,809 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
- CL
- Pockets
- 20 · best druggability 0.72
Structure
x-ray diffraction · 4 distinct chains · 38% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Galactoside 2-alpha-L-fucosyltransferase (EC 2.4.1.69) | protein | 459 | 39% helix, 15% strand | Q9SWH5 |
| B | Galactoside 2-alpha-L-fucosyltransferase (EC 2.4.1.69) | protein | 445 | 37% helix, 15% strand | Q9SWH5 |
| C | Galactoside 2-alpha-L-fucosyltransferase (EC 2.4.1.69) | protein | 448 | 38% helix, 15% strand | Q9SWH5 |
| D | Galactoside 2-alpha-L-fucosyltransferase (EC 2.4.1.69) | protein | 457 | 39% helix, 15% strand | Q9SWH5 |
Ligands and binding sites
- CL · Chloride ion · ion · 5 copies · chains A, C, D
- EDO · 1,2-ethanediol · additive · 5 copies · chains 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, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 690 | 0.72 | 0.79 | 85 | empty |
| 2 | 120 | 0.71 | 0.92 | 24 | empty |
| 3 | 346 | 0.71 | 0.83 | 49 | empty |
| 4 | 54 | 0.66 | 0.95 | 20 | empty |
| 5 | 86 | 0.66 | 0.92 | 27 | empty |
Interfaces
3 interfaces between chains.
- C–D · 1313 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 1305 Ų buried · 16 hydrogen bonds · protein-protein
- B–D · 376 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 disulfide (disulfide).
Compared structures
- 5KOP · Arabidopsis thaliana fucosyltransferase 1 (FUT1) in its apo-form · 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 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 5KOP · PDBe 5KOP · UniProt Q9SWH5
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