MolNFT v1 · #141176 · protein
Cryo-EM structure of L-fucokinase, GDP-fucose pyrophosphorylase (fkp) in bacteroides fragilis
5YYS · L-fucokinase, L-fucose-1-P guanylyltransferase: “Cryo-EM structure of L-fucokinase, GDP-fucose pyrophosphorylase (fkp) in bacteroides fragilis”. Electron microscopy, 20 pockets (best druggability 0.84). MolNFT v1 #141176 on…
- PDB
- 5YYS
- Type
- protein
- Length
- 3,244 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- L-fucokinase, L-fucose-1-P guanylyltransferase
- UniProt
- Q58T34
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 1 distinct chain · 29% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | L-fucokinase, L-fucose-1-P guanylyltransferase | protein | 811 | 29% helix, 6% strand | Q58T34 |
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1105 | 0.84 | 0.85 | 131 | empty |
| 2 | 835 | 0.84 | 0.86 | 120 | empty |
| 3 | 681 | 0.84 | 0.87 | 85 | empty |
| 4 | 1179 | 0.83 | 0.84 | 140 | empty |
| 5 | 926 | 0.83 | 0.84 | 114 | empty |
Interfaces
4 interfaces between chains.
- A–C · 1042 Ų buried · 18 hydrogen bonds · protein-protein
- B–D · 1020 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 662 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 657 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 5YYS · Cryo-EM structure of L-fucokinase, GDP-fucose pyrophosphorylase (FKP)in Bacteroides… · the same entry in another collection · chain A against A, 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 Q58T34
- Elsewhere: RCSB PDB 5YYS · PDBe 5YYS · UniProt Q58T34
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