Research workbench
Mouse POFUT1 in complex with O-glucosylated EGF(+) and GDP
Analyse Mouse POFUT1 in complex with O-glucosylated EGF(+) and GDP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5KY7
- Type
- protein
- Length
- 385 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GDP-fucose protein O-fucosyltransferase 1; EGF(+)
- EC
- 2.4.1.221
- UniProt
- Q91ZW2
- Ligands
- GDP, NAG, BGC
- Pockets
- 2 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | GDP-fucose protein O-fucosyltransferase 1 (EC 2.4.1.221) | protein | 347 | 43% helix, 16% strand | Q91ZW2 |
| B | EGF(+) | protein | 38 | 11% helix, 32% strand | — |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A
- BGC · beta-D-glucopyranose · sugar · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 483 | 0.73 | 0.82 | 42 | GDP |
| 2 | 207 | 0.56 | 0.79 | 39 | empty |
Interfaces
1 interface between chains.
- A–B · 882 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide, 3 glycan (disulfide, N-glycosylation, O-glycosylation).
Compared structures
- 5KY7 · mouse POFUT1 in complex with O-glucosylated EGF(+) and GDP · the same entry in another collection · chain A against A, TM-score 1.00
- Q91ZW2 · AlphaFold monomer V2.0 prediction for GDP-fucose protein O-fucosyltransferase 1 (Q91ZW2) · 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 Q91ZW2
- Elsewhere: RCSB PDB 5KY7 · PDBe 5KY7 · UniProt Q91ZW2
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