MolNFT v1 · #146821 · protein
Crystal structure of human 17BETA-hydroxysteroid dehydrogenase type 1 complexed with EM139
6DTP · Estradiol 17-beta-dehydrogenase 1: “Crystal structure of human 17BETA-hydroxysteroid dehydrogenase type 1 complexed with EM139”. X-ray diffraction, 1 ligand (EM9), 7 pockets (best druggability 0.80). MolNFT v1 #146821 on GenesisL1…
- PDB
- 6DTP
- Type
- protein
- Length
- 557 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Estradiol 17-beta-dehydrogenase 1
- EC
- 1.1.1.62
- UniProt
- P14061
- Ligands
- EM9
- Pockets
- 7 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 54% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Estradiol 17-beta-dehydrogenase 1 (EC 1.1.1.62) | protein | 279 | 55% helix, 15% strand | P14061 |
| B | Estradiol 17-beta-dehydrogenase 1 (EC 1.1.1.62) | protein | 278 | 53% helix, 15% strand | P14061 |
Ligands and binding sites
- EM9 · N-butyl-11-[(7alpha,9beta,13alpha,14beta,16alpha, 17alpha)-16-chloro-3,17-dihydroxyestra-1,3,5(10)-trien-7-yl]-N-methylundecanamide · ligand · chains A
- GOL · Glycerol · additive · 7 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, B
- PGE · Triethylene glycol · additive · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 117 | 0.80 | 0.98 | 28 | GOL, EDO |
| 2 | 624 | 0.73 | 0.80 | 61 | GOL, EM9 |
| 3 | 629 | 0.72 | 0.79 | 57 | empty |
| 4 | 64 | 0.48 | 0.84 | 15 | empty |
| 5 | 67 | 0.48 | 0.84 | 15 | PGE |
Interfaces
1 interface between chains.
- A–B · 2625 Ų buried · 40 hydrogen bonds · protein-protein
Compared structures
- 6DTP · Crystal structure of human 17BETA-hydroxysteroid dehydrogenase type 1 complexed with EM139 · the same entry in another collection · chain A against A, 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 6DTP · PDBe 6DTP · UniProt P14061
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