Research workbench
The refined three-dimensional structure of 3ALPHA,20BETA- hydroxysteroid dehydrogenase and possible roles of the residues conserved in short-chain dehydrogenases
Analyse The refined three-dimensional structure of 3ALPHA,20BETA- hydroxysteroid… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2HSD
- Type
- protein
- Length
- 1,012 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-alpha, 20 beta-hydroxysteroid dehydrogenase
- EC
- 1.1.1.53
- UniProt
- P19992
- Ligands
- NAD
- Pockets
- 9 · best druggability 0.88
Structure
x-ray diffraction · 1 distinct chain · 49% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | 3-alpha, 20 beta-hydroxysteroid dehydrogenase (EC 1.1.1.53) | protein | 253 | 49% helix, 16% strand | P19992 |
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
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 704 | 0.88 | 0.92 | 76 | empty |
| 2 | 581 | 0.73 | 0.80 | 56 | NAD |
| 3 | 681 | 0.73 | 0.79 | 54 | NAD |
| 4 | 555 | 0.73 | 0.80 | 51 | NAD |
| 5 | 593 | 0.71 | 0.79 | 47 | NAD |
Interfaces
6 interfaces between chains.
- A–D · 1773 Ų buried · 28 hydrogen bonds · protein-protein
- B–D · 1754 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 1702 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 1681 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 860 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 2HSD · The refined three-dimensional structure of 3ALPHA,20BETA-hydroxysteroid dehydrogenase and… · the same entry in another collection · chain A against A, TM-score 1.00
- P19992 · AlphaFold monomer V2.0 prediction for 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase… · a predicted model of the same protein · 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 P19992
- Elsewhere: RCSB PDB 2HSD · PDBe 2HSD · UniProt P19992
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