MolNFT v1 · #34580 · protein
Crystal structure of the 3-alpha-hydroxysteroid dehydrogenase from pseudomonas sp. B-0831 complexed with NADH
2DKN: “Crystal structure of the 3-alpha-hydroxysteroid dehydrogenase from pseudomonas sp. B-0831 complexed with NADH”. X-ray diffraction, 1 ligand (NAI), 3 pockets (best druggability 0.78). MolNFT v1 #34580 on GenesisL1: 3D structure…
- PDB
- 2DKN
- Type
- protein
- Length
- 480 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-alpha-hydroxysteroid dehydrogenase
- EC
- 1.1.1.50
- UniProt
- Q59718
- Ligands
- NAI
- Pockets
- 3 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 53% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3-alpha-hydroxysteroid dehydrogenase (EC 1.1.1.50) | protein | 254 | 53% helix, 14% strand | Q59718 |
| B | 3-alpha-hydroxysteroid dehydrogenase (EC 1.1.1.50) | protein | 226 | 54% helix, 15% strand | Q59718 |
Ligands and binding sites
- NAI · 1,4-dihydronicotinamide adenine dinucleotide · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 747 | 0.78 | 0.82 | 68 | NAI |
| 2 | 193 | 0.50 | 0.76 | 36 | empty |
| 3 | 108 | 0.39 | 0.75 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 1965 Ų buried · 26 hydrogen bonds · protein-protein
Compared structures
- 2DKN · Crystal structure of the 3-alpha-hydroxysteroid dehydrogenase from Pseudomonas sp. B-0831… · the same entry in another collection · chain A 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 Q59718
- Elsewhere: RCSB PDB 2DKN · PDBe 2DKN · UniProt Q59718
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