Research workbench
Crystal structure of human GDP-L-fucose synthase with bound NADP and product GDP-L-fucose
Analyse Crystal structure of human GDP-L-fucose synthase with bound NADP and product… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4BL5
- Type
- protein
- Length
- 3,805 residues
- Chains
- 12
- 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, GFB
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 6 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 | 314 | 47% helix, 16% strand | Q13630 |
| B | GDP-L-fucose synthase (EC 1.1.1.271) | protein | 320 | 43% helix, 17% strand | Q13630 |
| C, I | GDP-L-fucose synthase (EC 1.1.1.271) | protein | 321 | 43% helix, 16% strand | Q13630 |
| D, H | GDP-L-fucose synthase (EC 1.1.1.271) | protein | 315 | 43% helix, 17% strand | Q13630 |
| E, G, L | GDP-L-fucose synthase (EC 1.1.1.271) | protein | 320 | 44% helix, 16% strand | Q13630 |
| F, J, K | GDP-L-fucose synthase (EC 1.1.1.271) | protein | 313 | 45% helix, 15% strand | Q13630 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 12 copies · chains A, F, B, C, D, E, G, H, I, J, K, L
- GFB · Guanosine-5'-diphosphate-beta-L-fucopyranose · ligand · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- EDO · 1,2-ethanediol · additive · chains C, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 856 | 0.85 | 0.87 | 95 | empty |
| 2 | 543 | 0.83 | 0.89 | 68 | NAP, GFB |
| 3 | 526 | 0.83 | 0.89 | 71 | NAP, GFB |
| 4 | 525 | 0.83 | 0.89 | 66 | NAP, GFB |
| 5 | 532 | 0.83 | 0.89 | 72 | NAP, GFB |
Interfaces
17 interfaces between chains.
- B–D · 1253 Ų buried · 16 hydrogen bonds · protein-protein
- A–E · 1242 Ų buried · 18 hydrogen bonds · protein-protein
- K–L · 1236 Ų buried · 24 hydrogen bonds · protein-protein
- G–J · 1231 Ų buried · 14 hydrogen bonds · protein-protein
- H–I · 1205 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 4BL5 · Crystal structure of human GDP-L-fucose synthase with bound NADP and product GDP-L-fucose · the same entry in another collection · chain L against L, TM-score 1.00
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 4BL5 · PDBe 4BL5 · UniProt Q13630
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