Research workbench
Crystal structure of the ternary complex between a fungal 17BETA- hydroxysteroid dehydrogenase (holo form) and genistein
Analyse Crystal structure of the ternary complex between a fungal 17BETA… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4FJ1
- Type
- protein
- Length
- 1,039 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 17BETA-hydroxysteroid dehydrogenase
- EC
- 1.1.1.62
- UniProt
- O93874
- Ligands
- NAP, GEN
- Pockets
- 10 · best druggability 0.86
Structure
x-ray diffraction · 3 distinct chains · 49% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | 17BETA-hydroxysteroid dehydrogenase (EC 1.1.1.62) | protein | 261 | 49% helix, 14% strand | O93874 |
| B | 17BETA-hydroxysteroid dehydrogenase (EC 1.1.1.62) | protein | 259 | 50% helix, 14% strand | O93874 |
| C | 17BETA-hydroxysteroid dehydrogenase (EC 1.1.1.62) | protein | 258 | 50% helix, 14% strand | O93874 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains A, B, C, D
- GEN · Genistein · ligand · 2 copies · chains B, D
- DMS · Dimethyl sulfoxide · additive · 12 copies · chains A, B, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 985 | 0.86 | 0.88 | 75 | empty |
| 2 | 1099 | 0.84 | 0.85 | 131 | NAP, GEN, DMS |
| 3 | 396 | 0.80 | 0.89 | 59 | NAP, GEN, DMS |
| 4 | 290 | 0.73 | 0.86 | 40 | NAP |
| 5 | 92 | 0.71 | 0.94 | 22 | DMS |
Interfaces
6 interfaces between chains.
- A–B · 1869 Ų buried · 31 hydrogen bonds · protein-protein
- C–D · 1845 Ų buried · 32 hydrogen bonds · protein-protein
- B–D · 1695 Ų buried · 23 hydrogen bonds · protein-protein
- A–C · 1677 Ų buried · 23 hydrogen bonds · protein-protein
- B–C · 104 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 4FJ1 · Crystal Structure of the ternary complex between a fungal 17beta-hydroxysteroid… · the same entry in another collection · chain C against C, 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 O93874
- Elsewhere: RCSB PDB 4FJ1 · PDBe 4FJ1 · UniProt O93874
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