MolNFT v1 · #118026 · protein
The three-dimensional structure of clostridium absonum 7ALPHA- hydroxysteroid dehydrogenase
5EPO · 7-alpha-hydroxysteroid deydrogenase: “The three-dimensional structure of clostridium absonum 7ALPHA- hydroxysteroid dehydrogenase”. X-ray diffraction, 2 ligands (NAP, TUD), 11 pockets (best druggability 0.81). MolNFT v1 #118026 on…
- PDB
- 5EPO
- Type
- protein
- Length
- 1,044 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 7-alpha-hydroxysteroid deydrogenase
- UniProt
- G9FRD7
- Ligands
- NAP, TUD
- Pockets
- 11 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | 7-alpha-hydroxysteroid deydrogenase | protein | 261 | 49% helix, 16% strand | G9FRD7 |
| D | 7-alpha-hydroxysteroid deydrogenase | protein | 261 | 49% helix, 16% strand | G9FRD7 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains A, B, C, D
- TUD · Taurochenodeoxycholic acid · ligand · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 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 | 877 | 0.81 | 0.83 | 98 | empty |
| 2 | 629 | 0.79 | 0.84 | 54 | NAP, TUD |
| 3 | 649 | 0.79 | 0.84 | 54 | NAP, TUD |
| 4 | 624 | 0.78 | 0.84 | 54 | NAP, TUD |
| 5 | 636 | 0.78 | 0.83 | 55 | NAP, TUD |
Interfaces
6 interfaces between chains.
- B–C · 1815 Ų buried · 19 hydrogen bonds · protein-protein
- A–D · 1810 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 1624 Ų buried · 20 hydrogen bonds · protein-protein
- B–D · 1614 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 850 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 5EPO · The three-dimensional structure of Clostridium absonum 7alpha-hydroxysteroid dehydrogenase · the same entry in another collection · chain A against A, TM-score 1.00
- G9FRD7 · AlphaFold monomer V2.0 prediction for 7ALPHA-hydroxysteroid dehydrogenase (G9FRD7) · a predicted model of the same protein · chain D 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 G9FRD7
- Elsewhere: RCSB PDB 5EPO · PDBe 5EPO · UniProt G9FRD7
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