Research workbench
Crystal structure of a putative 2,5-diketo-D-gluconic acid reductase B
Analyse Crystal structure of a putative 2,5-diketo-D-gluconic acid reductase B in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3UP8
- Type
- protein
- Length
- 562 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative 2,5-diketo-D-gluconic acid reductase B
- EC
- 1.1.1.274
- UniProt
- Q92RC6
- Pockets
- 7 · best druggability 0.63
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Putative 2,5-diketo-D-gluconic acid reductase B (EC 1.1.1.274) | protein | 281 | 45% helix, 18% strand | Q92RC6 |
Ligands and binding sites
- ACT · Acetate ion · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 281 | 0.63 | 0.81 | 31 | empty |
| 2 | 148 | 0.60 | 0.83 | 32 | ACT |
| 3 | 298 | 0.57 | 0.77 | 38 | empty |
| 4 | 148 | 0.55 | 0.81 | 22 | empty |
| 5 | 79 | 0.54 | 0.86 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 853 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 modified (engineered).
Compared structures
- 3UP8 · Crystal structure of a putative 2,5-diketo-D-gluconic acid reductase B · 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 Q92RC6
- Elsewhere: RCSB PDB 3UP8 · PDBe 3UP8 · UniProt Q92RC6
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.