MolNFT v1 · #75557 · protein
Role of packing defects in the evolution of allostery and induced fit in human udp-glucose dehydrogenase.
3PTZ · Udp-glucose 6-dehydrogenase: “Role of packing defects in the evolution of allostery and induced fit in human udp-glucose dehydrogenase.”. X-ray diffraction, 2 ligands (NAD, UDX), 17 pockets (best druggability 0.78). MolNFT v1 #75557…
- PDB
- 3PTZ
- Type
- protein
- Length
- 2,744 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
- NAD, UDX
- Pockets
- 17 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Udp-glucose 6-dehydrogenase (EC 1.1.1.22) | protein | 458 | 45% helix, 15% strand | O60701 |
| B, C, D, F | Udp-glucose 6-dehydrogenase (EC 1.1.1.22) | protein | 457 | 46% helix, 15% strand | O60701 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 6 copies · chains A, B, C, D, E, F
- UDX · Uridine-5'-diphosphate-xylopyranose · ligand · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 847 | 0.78 | 0.81 | 89 | NAD, UDX |
| 2 | 860 | 0.78 | 0.81 | 106 | NAD, UDX |
| 3 | 891 | 0.78 | 0.81 | 109 | NAD, UDX |
| 4 | 747 | 0.77 | 0.81 | 81 | NAD, UDX |
| 5 | 800 | 0.77 | 0.81 | 88 | NAD, UDX |
Interfaces
9 interfaces between chains.
- A–B · 2671 Ų buried · 24 hydrogen bonds · protein-protein
- C–D · 2661 Ų buried · 26 hydrogen bonds · protein-protein
- E–F · 2651 Ų buried · 25 hydrogen bonds · protein-protein
- B–F · 812 Ų buried · 14 hydrogen bonds · protein-protein
- B–D · 793 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 3PTZ · Role of Packing Defects in the Evolution of Allostery and Induced Fit in Human… · 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 3PTZ · PDBe 3PTZ · UniProt O60701
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