MolNFT v1 · #47917 · protein
Structure of human hydroxysteroid dehydrogenase type 8, HSD17B8
2PD6 · Estradiol 17-beta-dehydrogenase 8: “Structure of human hydroxysteroid dehydrogenase type 8, HSD17B8”. X-ray diffraction, 1 ligand (NAD), 11 pockets (best druggability 0.78). MolNFT v1 #47917 on GenesisL1: 3D structure, binding sites…
- PDB
- 2PD6
- Type
- protein
- Length
- 953 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Estradiol 17-beta-dehydrogenase 8
- EC
- 1.1.1.62
- UniProt
- Q92506
- Ligands
- NAD
- Pockets
- 11 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 50% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Estradiol 17-beta-dehydrogenase 8 (EC 1.1.1.62) | protein | 233 | 49% helix, 18% strand | Q92506 |
| B | Estradiol 17-beta-dehydrogenase 8 (EC 1.1.1.62) | protein | 241 | 50% helix, 17% strand | Q92506 |
| C | Estradiol 17-beta-dehydrogenase 8 (EC 1.1.1.62) | protein | 237 | 52% helix, 17% strand | Q92506 |
| D | Estradiol 17-beta-dehydrogenase 8 (EC 1.1.1.62) | protein | 242 | 50% helix, 16% strand | Q92506 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 675 | 0.78 | 0.83 | 70 | empty |
| 2 | 347 | 0.73 | 0.84 | 48 | NAD |
| 3 | 231 | 0.70 | 0.86 | 41 | NAD |
| 4 | 218 | 0.68 | 0.85 | 44 | NAD |
| 5 | 201 | 0.64 | 0.83 | 35 | NAD |
Interfaces
4 interfaces between chains.
- B–C · 1680 Ų buried · 24 hydrogen bonds · protein-protein
- A–D · 1644 Ų buried · 27 hydrogen bonds · protein-protein
- A–B · 1294 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 1271 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 2PD6 · Structure of human hydroxysteroid dehydrogenase type 8, HSD17B8 · the same entry in another collection · chain D against D, TM-score 1.00
- Q92506 · AlphaFold monomer V2.0 prediction for estradiol 17-beta-dehydrogenase 8 (Q92506) · a predicted model of the same protein · chain D against A, 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 Q92506
- Elsewhere: RCSB PDB 2PD6 · PDBe 2PD6 · UniProt Q92506
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.