MolNFT v1 · #79781 · protein
Crystal structure of human udp-glucose dehydrogenase
3TDK · Udp-glucose 6-dehydrogenase: “Crystal structure of human udp-glucose dehydrogenase”. X-ray diffraction, 2 ligands (NAD, UPG), 20 pockets (best druggability 0.79). MolNFT v1 #79781 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3TDK
- 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
- NAD, UPG
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, G, H, L, F, D, C, J, I | Udp-glucose 6-dehydrogenase (EC 1.1.1.22) | protein | 460 | 45% helix, 15% strand | O60701 |
| K, E | Udp-glucose 6-dehydrogenase (EC 1.1.1.22) | protein | 458 | 43% helix, 15% strand | O60701 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 12 copies · chains A, B, G, H, L, K, F, E, D, C, J, I
- UPG · Uridine-5'-diphosphate-glucose · ligand · 12 copies · chains A, B, G, H, L, K, F, E, D, C, J, I
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 | 899 | 0.79 | 0.82 | 108 | UPG, NAD |
| 2 | 859 | 0.79 | 0.82 | 98 | NAD, UPG |
| 3 | 977 | 0.79 | 0.81 | 110 | NAD, UPG |
| 4 | 892 | 0.79 | 0.81 | 105 | NAD, UPG |
| 5 | 941 | 0.79 | 0.81 | 112 | NAD, UPG |
Interfaces
22 interfaces between chains.
- D–C · 2719 Ų buried · 24 hydrogen bonds · protein-protein
- F–E · 2719 Ų buried · 26 hydrogen bonds · protein-protein
- L–K · 2709 Ų buried · 24 hydrogen bonds · protein-protein
- J–I · 2703 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 2691 Ų buried · 27 hydrogen bonds · protein-protein
Compared structures
- 3TDK · Crystal Structure of Human UDP-Glucose Dehydrogenase · the same entry in another collection · chain I against I, 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 3TDK · PDBe 3TDK · UniProt O60701
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