Research workbench
Crystal structure of human GDP-L-fucose synthase with bound NADP and GDP, tetragonal crystal form
Analyse Crystal structure of human GDP-L-fucose synthase with bound NADP and GDP… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4B8W
- Type
- protein
- Length
- 619 residues
- Chains
- 2
- 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
- NAP, GDP
- Pockets
- 5 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | GDP-L-fucose synthase (EC 1.1.1.271) | protein | 319 | 44% helix, 15% strand | Q13630 |
| B | GDP-L-fucose synthase (EC 1.1.1.271) | protein | 300 | 44% helix, 17% strand | Q13630 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
- GDP · Guanosine-5'-diphosphate · ligand · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 623 | 0.82 | 0.87 | 76 | NAP, GDP |
| 2 | 771 | 0.74 | 0.79 | 80 | NAP, GDP |
| 3 | 70 | 0.49 | 0.84 | 20 | empty |
| 4 | 55 | 0.32 | 0.77 | 14 | empty |
| 5 | 57 | 0.29 | 0.75 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1209 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 4B8W · Crystal structure of human GDP-L-fucose synthase with bound NADP and GDP, tetragonal… · the same entry in another collection · chain A against A, TM-score 1.00
- Q13630 · AlphaFold monomer V2.0 prediction for GDP-L-fucose synthase (Q13630) · a predicted model of the same protein · chain B 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 Q13630
- Elsewhere: RCSB PDB 4B8W · PDBe 4B8W · UniProt Q13630
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