Research workbench
Crystal structure of human POFUT2 E54A mutant in complex with GDP- fucose
Analyse Crystal structure of human POFUT2 E54A mutant 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
- 4AP6
- Type
- protein
- Length
- 1,555 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GDP-fucose protein O-fucosyltransferase 2
- EC
- 2.4.1.221
- UniProt
- Q9Y2G5
- Ligands
- GFB, NAG, CL
- Pockets
- 20 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | GDP-fucose protein O-fucosyltransferase 2 (EC 2.4.1.221) | protein | 389 | 35% helix, 21% strand | Q9Y2G5 |
| C | GDP-fucose protein O-fucosyltransferase 2 (EC 2.4.1.221) | protein | 388 | 36% helix, 20% strand | Q9Y2G5 |
Ligands and binding sites
- GFB · Guanosine-5'-diphosphate-beta-L-fucopyranose · ligand · 4 copies · chains A, B, C, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, B, C
- CL · Chloride ion · ion · 4 copies · chains A, 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, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 613 | 0.72 | 0.79 | 52 | GFB, CL |
| 2 | 65 | 0.72 | 0.97 | 18 | empty |
| 3 | 63 | 0.71 | 0.97 | 19 | empty |
| 4 | 63 | 0.71 | 0.97 | 19 | empty |
| 5 | 63 | 0.71 | 0.97 | 19 | empty |
Interfaces
3 interfaces between chains.
- A–B · 693 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 661 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 566 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 6 glycan (disulfide, N-glycosylation).
Compared structures
- 4AP6 · Crystal structure of human POFUT2 E54A mutant in complex with GDP- fucose · the same entry in another collection · chain A against A, TM-score 1.00
- Q9Y2G5 · AlphaFold monomer V2.0 prediction for GDP-fucose protein O-fucosyltransferase 2 (Q9Y2G5) · a predicted model of the same protein · chain C against A, TM-score 0.98
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 Q9Y2G5
- Elsewhere: RCSB PDB 4AP6 · PDBe 4AP6 · UniProt Q9Y2G5
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