Research workbench
The first structure of udp-glucose dehydrogenase (udpgdh) reveals the catalytic residues necessary for the two-fold oxidation
Analyse The first structure of udp-glucose dehydrogenase (udpgdh) reveals the catalytic… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1DLI
- Type
- protein
- Length
- 402 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Udp-glucose dehydrogenase
- EC
- 1.1.1.22
- UniProt
- P0C0F4
- Ligands
- NAD, UDX, SO4
- Pockets
- 3 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Udp-glucose dehydrogenase (EC 1.1.1.22) | protein | 402 | 45% helix, 13% strand | P0C0F4 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · chains A
- UDX · Uridine-5'-diphosphate-xylopyranose · ligand · chains A
- SO4 · Sulfate ion · ion · 3 copies · chains A
- GOL · Glycerol · additive · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 558 | 0.77 | 0.84 | 74 | NAD, UDX, GOL |
| 2 | 55 | 0.37 | 0.80 | 17 | empty |
| 3 | 62 | 0.33 | 0.76 | 13 | empty |
Compared structures
- 1DLI · The first structure of udp-glucose dehydrogenase (udpgdh) reveals the catalytic residues… · the same entry in another collection · chain A against A, TM-score 1.00
- P0C0F4 · AlphaFold monomer V2.0 prediction for udp-glucose 6-dehydrogenase (P0C0F4) · a predicted model of the same protein · 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 P0C0F4
- Elsewhere: RCSB PDB 1DLI · PDBe 1DLI · UniProt P0C0F4
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