Research workbench
Structure of human fx protein, the key enzyme in the biosynthesis of GDP-L-fucose
Analyse Structure of human fx protein, the key enzyme in the biosynthesis of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4E5Y
- Type
- protein
- Length
- 1,224 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GDP-L-fucose synthase
- EC
- 1.1.1.271
- UniProt
- Q13630
- Ligands
- NDP
- Pockets
- 12 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 38% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | GDP-L-fucose synthase (EC 1.1.1.271) | protein | 307 | 40% helix, 15% strand | Q13630 |
| B | GDP-L-fucose synthase (EC 1.1.1.271) | protein | 309 | 41% helix, 12% strand | Q13630 |
| C | GDP-L-fucose synthase (EC 1.1.1.271) | protein | 290 | 34% helix, 14% strand | Q13630 |
| D | GDP-L-fucose synthase (EC 1.1.1.271) | protein | 318 | 38% helix, 14% strand | Q13630 |
Ligands and binding sites
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1016 | 0.82 | 0.83 | 85 | NDP |
| 2 | 769 | 0.82 | 0.85 | 93 | empty |
| 3 | 872 | 0.81 | 0.83 | 74 | NDP |
| 4 | 440 | 0.79 | 0.87 | 46 | NDP |
| 5 | 837 | 0.79 | 0.82 | 79 | NDP |
Interfaces
5 interfaces between chains.
- A–B · 1332 Ų buried · 27 hydrogen bonds · protein-protein
- C–D · 1332 Ų buried · 26 hydrogen bonds · protein-protein
- B–D · 588 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 477 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 48 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4E5Y · Structure of human FX protein, the key enzyme in the biosynthesis of GDP-L-fucose · the same entry in another collection · chain D against D, TM-score 1.00
- Q13630 · AlphaFold monomer V2.0 prediction for GDP-L-fucose synthase (Q13630) · a predicted model of the same protein · chain A 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 Q13630
- Elsewhere: RCSB PDB 4E5Y · PDBe 4E5Y · UniProt Q13630
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