Research workbench
Bcec mutation Y10K
Analyse Bcec mutation Y10K in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2Y0D
- Type
- protein
- Length
- 1,807 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
- 18 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 46% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Udp-glucose dehydrogenase (EC 1.1.1.22) | protein | 455 | 46% helix, 13% strand | C9E261 |
| B | Udp-glucose dehydrogenase (EC 1.1.1.22) | protein | 448 | 46% helix, 14% strand | C9E261 |
| C | Udp-glucose dehydrogenase (EC 1.1.1.22) | protein | 451 | 46% helix, 13% strand | C9E261 |
| D | Udp-glucose dehydrogenase (EC 1.1.1.22) | protein | 453 | 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 · 8 copies · chains A, D, C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1076 | 0.81 | 0.82 | 114 | UGA |
| 2 | 919 | 0.80 | 0.82 | 110 | UGA, SO4 |
| 3 | 1049 | 0.79 | 0.80 | 84 | UGA |
| 4 | 965 | 0.77 | 0.80 | 80 | UGA, SO4 |
| 5 | 1065 | 0.73 | 0.77 | 93 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2796 Ų buried · 31 hydrogen bonds · protein-protein
- C–D · 2740 Ų buried · 30 hydrogen bonds · protein-protein
- A–C · 803 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 776 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 163 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 2Y0D · BceC mutation Y10K · 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 2Y0D · PDBe 2Y0D · UniProt C9E261
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