Research workbench
Structure of human POFUT1 in complex with GDP-fucose
Analyse Structure of human POFUT1 in complex with GDP-fucose in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5UXH
- Type
- protein
- Length
- 702 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GDP-fucose protein O-fucosyltransferase 1
- EC
- 2.4.1.221
- UniProt
- Q9H488
- Ligands
- GFB, NAG
- Pockets
- 5 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | GDP-fucose protein O-fucosyltransferase 1 (EC 2.4.1.221) | protein | 349 | 42% helix, 17% strand | Q9H488 |
| B | GDP-fucose protein O-fucosyltransferase 1 (EC 2.4.1.221) | protein | 353 | 40% helix, 15% strand | Q9H488 |
Ligands and binding sites
- GFB · Guanosine-5'-diphosphate-beta-L-fucopyranose · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1176 | 0.81 | 0.82 | 109 | empty |
| 2 | 371 | 0.61 | 0.77 | 34 | GFB |
| 3 | 342 | 0.61 | 0.78 | 33 | GFB |
| 4 | 79 | 0.36 | 0.76 | 19 | empty |
| 5 | 64 | 0.31 | 0.74 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 517 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 5UXH · Structure of Human POFUT1 in complex with GDP-fucose · the same entry in another collection · chain A against A, TM-score 1.00
- Q9H488 · AlphaFold monomer V2.0 prediction for GDP-fucose protein O-fucosyltransferase 1 (Q9H488) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q9H488
- Elsewhere: RCSB PDB 5UXH · PDBe 5UXH · UniProt Q9H488
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.