Research workbench
Crystal structure of 5BETA-reductase (AKR1D1) in complex with NADP+ and 5BETA-pregnan-3,20-dione
Analyse Crystal structure of 5BETA-reductase (AKR1D1) in complex with NADP+ and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3CAV
- 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, CI2
- Pockets
- 5 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 15% 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, 15% strand | P51857 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
- CI2 · (5beta)-pregnane-3,20-dione · ligand · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 5 copies · chains A, B
- BME · Beta-mercaptoethanol · additive · 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 | 493 | 0.76 | 0.84 | 45 | NAP, CI2 |
| 2 | 584 | 0.76 | 0.82 | 53 | NAP, CI2, EDO |
| 3 | 682 | 0.75 | 0.81 | 68 | empty |
| 4 | 76 | 0.45 | 0.82 | 24 | empty |
| 5 | 50 | 0.35 | 0.79 | 11 | empty |
Interfaces
1 interface between chains.
- A–B · 488 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (additive adduct).
Compared structures
- 3CAV · Crystal structure of 5beta-reductase (AKR1D1) 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 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 P51857
- Elsewhere: RCSB PDB 3CAV · PDBe 3CAV · UniProt P51857
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