Research workbench
Crystal structure of 5BETA-reductase (AKR1D1) in complex with NADPH
Analyse Crystal structure of 5BETA-reductase (AKR1D1) in complex with NADPH in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3CAQ
- Type
- protein
- Length
- 649 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
- NDP
- Pockets
- 4 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3-oxo-5-beta-steroid 4-dehydrogenase (EC 1.3.1.3) | protein | 325 | 38% helix, 15% strand | P51857 |
| B | 3-oxo-5-beta-steroid 4-dehydrogenase (EC 1.3.1.3) | protein | 324 | 38% helix, 15% strand | P51857 |
Ligands and binding sites
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, B
- BME · Beta-mercaptoethanol · additive · 2 copies · chains A, B
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1131 | 0.81 | 0.82 | 110 | EDO, NDP, MPD |
| 2 | 566 | 0.76 | 0.82 | 54 | NDP, EDO, MPD |
| 3 | 51 | 0.32 | 0.77 | 10 | empty |
| 4 | 55 | 0.25 | 0.73 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 429 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (additive adduct).
Compared structures
- 3CAQ · Crystal structure of 5beta-reductase (AKR1D1) in complex with NADPH · 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 3CAQ · PDBe 3CAQ · UniProt P51857
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.