Research workbench
Structure of human udp-glucose dehydrogenase complexed with NADH and udp-glucose
Analyse Structure of human udp-glucose dehydrogenase complexed with NADH and udp-glucose in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2Q3E
- Type
- protein
- Length
- 5,516 residues
- Chains
- 12
- 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
- NAI, UPG, CL
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 46% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, F, G, I, J, K, L | Udp-glucose 6-dehydrogenase (EC 1.1.1.22) | protein | 460 | 46% helix, 14% strand | O60701 |
| D | Udp-glucose 6-dehydrogenase (EC 1.1.1.22) | protein | 458 | 46% helix, 14% strand | O60701 |
| E, H | Udp-glucose 6-dehydrogenase (EC 1.1.1.22) | protein | 459 | 45% helix, 14% strand | O60701 |
Ligands and binding sites
- NAI · 1,4-dihydronicotinamide adenine dinucleotide · ligand · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- UPG · Uridine-5'-diphosphate-glucose · ligand · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- CL · Chloride ion · ion · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 880 | 0.80 | 0.82 | 99 | NAI, UPG |
| 2 | 825 | 0.80 | 0.83 | 97 | NAI, UPG |
| 3 | 814 | 0.80 | 0.83 | 94 | NAI, UPG |
| 4 | 861 | 0.79 | 0.82 | 99 | NAI, UPG |
| 5 | 883 | 0.79 | 0.82 | 98 | NAI, UPG |
Interfaces
27 interfaces between chains.
- G–H · 2796 Ų buried · 27 hydrogen bonds · protein-protein
- I–J · 2788 Ų buried · 27 hydrogen bonds · protein-protein
- A–B · 2788 Ų buried · 24 hydrogen bonds · protein-protein
- C–D · 2786 Ų buried · 26 hydrogen bonds · protein-protein
- E–F · 2778 Ų buried · 27 hydrogen bonds · protein-protein
Compared structures
- 2Q3E · Structure of human UDP-glucose dehydrogenase complexed with NADH and UDP-glucose · the same entry in another collection · chain G against G, 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 O60701
- Elsewhere: RCSB PDB 2Q3E · PDBe 2Q3E · UniProt O60701
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