MolNFT v1 · #49179 · protein
Crystal structure of human udp-glucose dehydrogenase product complex with udp-glucuronate
2QG4 · Udp-glucose 6-dehydrogenase: “Crystal structure of human udp-glucose dehydrogenase product complex with udp-glucuronate”. X-ray diffraction, 3 ligands (NAD, UGA, CL), 17 pockets (best druggability 0.79). MolNFT v1 #49179 on…
- PDB
- 2QG4
- Type
- protein
- Length
- 3,682 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Udp-glucose 6-dehydrogenase
- EC
- 1.1.1.22
- UniProt
- O60701
- Ligands
- NAD, UGA, CL
- Pockets
- 17 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 46% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, G | Udp-glucose 6-dehydrogenase (EC 1.1.1.22) | protein | 460 | 45% helix, 15% strand | O60701 |
| B, D, F, H | Udp-glucose 6-dehydrogenase (EC 1.1.1.22) | protein | 461 | 46% helix, 14% strand | O60701 |
| C, E | Udp-glucose 6-dehydrogenase (EC 1.1.1.22) | protein | 459 | 46% helix, 15% strand | O60701 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- UGA · Uridine-5'-diphosphate-glucuronic acid · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- CL · Chloride ion · ion · 8 copies · chains B, D, F, H
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 893 | 0.79 | 0.82 | 102 | NAD, UGA |
| 2 | 842 | 0.79 | 0.82 | 97 | NAD, UGA |
| 3 | 810 | 0.79 | 0.82 | 97 | NAD, UGA |
| 4 | 861 | 0.77 | 0.80 | 92 | NAD, UGA |
| 5 | 796 | 0.77 | 0.81 | 88 | NAD, UGA |
Interfaces
8 interfaces between chains.
- C–D · 2842 Ų buried · 31 hydrogen bonds · protein-protein
- G–H · 2840 Ų buried · 33 hydrogen bonds · protein-protein
- E–F · 2840 Ų buried · 31 hydrogen bonds · protein-protein
- A–B · 2839 Ų buried · 33 hydrogen bonds · protein-protein
- B–D · 208 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 2QG4 · Crystal structure of human UDP-glucose dehydrogenase product complex with UDP-glucuronate · the same entry in another collection · chain H against H, TM-score 1.00
- O60701 · AlphaFold monomer V2.0 prediction for udp-glucose 6-dehydrogenase (O60701) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 O60701
- Elsewhere: RCSB PDB 2QG4 · PDBe 2QG4 · UniProt O60701
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