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Crystal structure of human 17BETA-hsd type 1 in ternary complex with pbrm and NADP+
Analyse Crystal structure of human 17BETA-hsd type 1 in ternary complex with pbrm and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6CGE
- Type
- protein
- Length
- 556 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
- NAP, F0D
- Pockets
- 5 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 53% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Estradiol 17-beta-dehydrogenase 1 (EC 1.1.1.62) | protein | 279 | 53% helix, 15% strand | P14061 |
| B | Estradiol 17-beta-dehydrogenase 1 (EC 1.1.1.62) | protein | 277 | 54% helix, 15% strand | P14061 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
- F0D · 3-{[(14beta,16alpha,17alpha)-3-(2-bromoethyl)-17-hydroxyestra-1,3,5(10)-trien-16-yl]methyl}benzamide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 118 | 0.77 | 0.96 | 27 | empty |
| 2 | 747 | 0.76 | 0.80 | 57 | NAP, F0D |
| 3 | 622 | 0.72 | 0.79 | 54 | NAP, F0D |
| 4 | 69 | 0.47 | 0.83 | 16 | empty |
| 5 | 52 | 0.29 | 0.75 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 2781 Ų buried · 43 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 6CGE · Crystal structure of human 17beta-HSD type 1 in ternary complex with PBRM and NADP+ · 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 6CGE · PDBe 6CGE · UniProt P14061
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