MolNFT v1 · #137524 · protein
Human udp-glucose dehydrogenase with udp-xylose bound to the co-enzyme site
5VR8 · Udp-glucose 6-dehydrogenase: “Human udp-glucose dehydrogenase with udp-xylose bound to the co-enzyme site”. X-ray diffraction, 2 ligands (UDX, ADP), 20 pockets (best druggability 0.78). MolNFT v1 #137524 on GenesisL1: 3D structure…
- PDB
- 5VR8
- Type
- protein
- Length
- 2,753 residues
- Chains
- 6
- 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
- UDX, ADP
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 5 distinct chains · 46% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Udp-glucose 6-dehydrogenase (EC 1.1.1.22) | protein | 460 | 46% helix, 15% strand | O60701 |
| B | Udp-glucose 6-dehydrogenase (EC 1.1.1.22) | protein | 459 | 46% helix, 15% strand | O60701 |
| C | Udp-glucose 6-dehydrogenase (EC 1.1.1.22) | protein | 462 | 46% helix, 15% strand | O60701 |
| D, E | Udp-glucose 6-dehydrogenase (EC 1.1.1.22) | protein | 457 | 46% helix, 14% strand | O60701 |
| F | Udp-glucose 6-dehydrogenase (EC 1.1.1.22) | protein | 458 | 46% helix, 14% strand | O60701 |
Ligands and binding sites
- UDX · Uridine-5'-diphosphate-xylopyranose · ligand · 10 copies · chains A, B, C, E, D, F
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains C, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 878 | 0.78 | 0.81 | 101 | UDX |
| 2 | 831 | 0.78 | 0.81 | 100 | UDX |
| 3 | 689 | 0.76 | 0.82 | 94 | ADP, UDX |
| 4 | 776 | 0.76 | 0.81 | 91 | ADP, UDX |
| 5 | 773 | 0.76 | 0.81 | 86 | UDX |
Interfaces
9 interfaces between chains.
- A–B · 2661 Ų buried · 23 hydrogen bonds · protein-protein
- D–F · 2653 Ų buried · 24 hydrogen bonds · protein-protein
- C–E · 2650 Ų buried · 24 hydrogen bonds · protein-protein
- A–F · 755 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 749 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 5VR8 · Human UDP-Glucose Dehydrogenase with UDP-Xylose Bound to the Co-enzyme Site · the same entry in another collection · chain F against F, TM-score 1.00
- O60701 · AlphaFold monomer V2.0 prediction for udp-glucose 6-dehydrogenase (O60701) · a predicted model of the same protein · chain A 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 5VR8 · PDBe 5VR8 · UniProt O60701
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.