Research workbench
Crystal structure of human GDP-L-fucose synthase with bound NADP and GDP, rhombohedral 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
- 4B8Z
- Type
- protein
- Length
- 1,254 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
- NAP, GDP
- Pockets
- 12 · best druggability 0.85
Structure
x-ray diffraction · 3 distinct chains · 43% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | GDP-L-fucose synthase (EC 1.1.1.271) | protein | 308 | 44% helix, 16% strand | Q13630 |
| B | GDP-L-fucose synthase (EC 1.1.1.271) | protein | 320 | 43% helix, 16% strand | Q13630 |
| C, D | GDP-L-fucose synthase (EC 1.1.1.271) | protein | 313 | 43% helix, 16% strand | Q13630 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains A, B, C, D
- GDP · Guanosine-5'-diphosphate · 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 | 975 | 0.85 | 0.86 | 129 | NAP, GDP |
| 2 | 518 | 0.83 | 0.89 | 63 | NAP, GDP |
| 3 | 525 | 0.83 | 0.89 | 68 | NAP, GDP |
| 4 | 625 | 0.83 | 0.87 | 76 | NAP, GDP |
| 5 | 416 | 0.70 | 0.82 | 51 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1154 Ų buried · 16 hydrogen bonds · protein-protein
- B–D · 520 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 74 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4B8Z · Crystal structure of human GDP-L-fucose synthase with bound NADP and GDP, rhombohedral… · 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 C 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 4B8Z · PDBe 4B8Z · UniProt Q13630
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