MolNFT v1 · #6481 · protein
Human 17-beta-hydroxysteroid-dehydrogenase type 1 mutant H221L complexed with NAD+
1FDV · 17-beta-hydroxysteroid dehydrogenase: “Human 17-beta-hydroxysteroid-dehydrogenase type 1 mutant H221L complexed with NAD+”. X-ray diffraction, 2 ligands (NAD, SO4), 18 pockets (best druggability 0.81). MolNFT v1 #6481 on GenesisL1…
- PDB
- 1FDV
- Type
- protein
- Length
- 1,120 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 17-beta-hydroxysteroid dehydrogenase
- EC
- 1.1.1.62
- UniProt
- P14061
- Ligands
- NAD, SO4
- Pockets
- 18 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 54% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | 17-beta-hydroxysteroid dehydrogenase (EC 1.1.1.62) | protein | 285 | 55% helix, 14% strand | P14061 |
| B, D | 17-beta-hydroxysteroid dehydrogenase (EC 1.1.1.62) | protein | 275 | 54% helix, 15% strand | P14061 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 4 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 569 | 0.81 | 0.87 | 67 | NAD, SO4 |
| 2 | 752 | 0.80 | 0.84 | 82 | NAD, SO4 |
| 3 | 132 | 0.80 | 0.97 | 29 | empty |
| 4 | 141 | 0.80 | 0.97 | 29 | empty |
| 5 | 708 | 0.73 | 0.79 | 63 | NAD |
Interfaces
3 interfaces between chains.
- A–B · 2701 Ų buried · 31 hydrogen bonds · protein-protein
- C–D · 2637 Ų buried · 34 hydrogen bonds · protein-protein
- A–C · 493 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 1FDV · Human 17-beta-hydroxysteroid-dehydrogenase type 1 mutant H221L complexed with NAD+ · the same entry in another collection · chain D against D, TM-score 1.00
- P14061 · AlphaFold monomer V2.0 prediction for 17-beta-hydroxysteroid dehydrogenase type 1 (P14061) · 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 P14061
- Elsewhere: RCSB PDB 1FDV · PDBe 1FDV · UniProt P14061
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