Research workbench
Bcec and the final step of ugds reaction
Analyse Bcec and the final step of ugds reaction in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2Y0E
- Type
- protein
- Length
- 1,821 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Udp-glucose dehydrogenase
- EC
- 1.1.1.22
- UniProt
- C9E261
- Ligands
- UGA, SO4
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 47% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Udp-glucose dehydrogenase (EC 1.1.1.22) | protein | 461 | 46% helix, 13% strand | C9E261 |
| B | Udp-glucose dehydrogenase (EC 1.1.1.22) | protein | 451 | 47% helix, 14% strand | C9E261 |
| C | Udp-glucose dehydrogenase (EC 1.1.1.22) | protein | 455 | 46% helix, 14% strand | C9E261 |
| D | Udp-glucose dehydrogenase (EC 1.1.1.22) | protein | 454 | 46% helix, 13% strand | C9E261 |
Ligands and binding sites
- UGA · Uridine-5'-diphosphate-glucuronic acid · ligand · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 14 copies · chains A, C, D, B
- GOL · Glycerol · additive · 6 copies · chains A, B, C, D
- ACT · Acetate ion · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 575 | 0.80 | 0.85 | 68 | UGA, ACT |
| 2 | 585 | 0.79 | 0.85 | 68 | UGA |
| 3 | 537 | 0.78 | 0.85 | 70 | UGA |
| 4 | 436 | 0.77 | 0.86 | 52 | UGA, ACT, GOL |
| 5 | 554 | 0.73 | 0.81 | 50 | SO4 |
Interfaces
6 interfaces between chains.
- C–D · 2779 Ų buried · 32 hydrogen bonds · protein-protein
- A–B · 2737 Ų buried · 30 hydrogen bonds · protein-protein
- A–C · 853 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 751 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 200 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 2Y0E · BceC and the final step of UGDs reaction · 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 C9E261
- Elsewhere: RCSB PDB 2Y0E · PDBe 2Y0E · UniProt C9E261
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