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Crystal structure of 5BETA-reductase (AKR1D1) E120H mutant in complex with NADP+ and epiandrosterone
Analyse Crystal structure of 5BETA-reductase (AKR1D1) E120H mutant in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3UZX
- Type
- protein
- Length
- 650 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-oxo-5-beta-steroid 4-dehydrogenase
- EC
- 1.3.1.3
- UniProt
- P51857
- Ligands
- NAP, AOM, AOX, CL
- Pockets
- 6 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 3-oxo-5-beta-steroid 4-dehydrogenase (EC 1.3.1.3) | protein | 325 | 38% helix, 16% strand | P51857 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
- AOM · 5-alpha-androstane-3-beta,17beta-diol · ligand · chains A
- AOX · (3Beta,5alpha)-3-Hydroxyandrostan-17-one · ligand · chains B
- CL · Chloride ion · ion · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 484 | 0.74 | 0.83 | 50 | NAP, AOM |
| 2 | 455 | 0.74 | 0.83 | 49 | NAP, AOX, CL |
| 3 | 523 | 0.67 | 0.78 | 58 | empty |
| 4 | 262 | 0.54 | 0.76 | 31 | empty |
| 5 | 72 | 0.46 | 0.82 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 481 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 3UZX · Crystal structure of 5beta-reductase (AKR1D1) E120H mutant in complex with NADP+ and… · the same entry in another collection · chain A against A, TM-score 1.00
- P51857 · AlphaFold monomer V2.0 prediction for aldo-keto reductase family 1 member D1 (P51857) · a predicted model of the same protein · chain B 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 P51857
- Elsewhere: RCSB PDB 3UZX · PDBe 3UZX · UniProt P51857
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