Research workbench
Crystal structure of human liver 5BETA-reductase (AKR1D1) in complex with NADP and cortisone. resolution 1.90 a.
Analyse Crystal structure of human liver 5BETA-reductase (AKR1D1) in complex with NADP… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3CMF
- 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, PDN
- Pockets
- 5 · best druggability 0.76
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
- PDN · 17,21-dihydroxypregna-1,4-diene-3,11,20-trione · 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 | 532 | 0.76 | 0.83 | 50 | NAP, PDN |
| 2 | 487 | 0.75 | 0.83 | 51 | NAP, PDN |
| 3 | 366 | 0.64 | 0.79 | 48 | empty |
| 4 | 206 | 0.49 | 0.75 | 23 | empty |
| 5 | 52 | 0.46 | 0.85 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 455 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 3CMF · Crystal structure of human liver 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 A 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 3CMF · PDBe 3CMF · UniProt P51857
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