MolNFT v1 · #125024 · protein
The structure of arabidopsis thaliana FUT1 in complex with GDP
5KWK · Galactoside 2-alpha-L-fucosyltransferase: “The structure of arabidopsis thaliana FUT1 in complex with GDP”. X-ray diffraction, 1 ligand (GDP), 9 pockets (best druggability 0.69). MolNFT v1 #125024 on GenesisL1: 3D structure, binding…
- PDB
- 5KWK
- Type
- protein
- Length
- 897 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
- 9 · best druggability 0.69
Structure
x-ray diffraction · 2 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 | 440 | 39% helix, 15% strand | Q9SWH5 |
| B | Galactoside 2-alpha-L-fucosyltransferase (EC 2.4.1.69) | protein | 457 | 39% helix, 15% strand | Q9SWH5 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 16 copies · chains A, B
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 2 copies · chains A, B
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 311 | 0.69 | 0.83 | 48 | GDP |
| 2 | 160 | 0.66 | 0.87 | 37 | empty |
| 3 | 80 | 0.62 | 0.90 | 24 | empty |
| 4 | 64 | 0.59 | 0.90 | 19 | EDO |
| 5 | 317 | 0.57 | 0.76 | 42 | GOL, EDO |
Interfaces
1 interface between chains.
- A–B · 468 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 5KWK · The structure of Arabidopsis thaliana FUT1 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 5KWK · PDBe 5KWK · UniProt Q9SWH5
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