Research workbench
Crystal structure of H3ALPHA-hydroxysteroid dehydrogenase type 3 mutant Y24A in complex with NADP+ and epi-testosterone
Analyse Crystal structure of H3ALPHA-hydroxysteroid dehydrogenase type 3 mutant Y24A in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2IPJ
- Type
- protein
- Length
- 642 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aldo-keto reductase family 1 member C2
- EC
- 1.-.-.-, 1.3.1.20, 1.1.1.213
- UniProt
- P52895
- Ligands
- NAP, FFA, SO4
- Pockets
- 8 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Aldo-keto reductase family 1 member C2 (EC 1.-.-.-, 1.3.1.20, 1.1.1.213) | protein | 321 | 40% helix, 17% strand | P52895 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
- FFA · (10alpha,13alpha,14beta,17alpha)-17-hydroxyandrost-4-en-3-one · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 3 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 7 copies · chains A, B
- BME · Beta-mercaptoethanol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 649 | 0.82 | 0.86 | 57 | EDO |
| 2 | 490 | 0.77 | 0.85 | 44 | NAP, FFA |
| 3 | 530 | 0.76 | 0.83 | 45 | NAP, FFA |
| 4 | 85 | 0.54 | 0.85 | 19 | BME |
| 5 | 67 | 0.46 | 0.82 | 15 | EDO |
Interfaces
1 interface between chains.
- A–B · 1222 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (additive adduct).
Compared structures
- 2IPJ · Crystal structure of h3alpha-hydroxysteroid dehydrogenase type 3 mutant Y24A in complex… · the same entry in another collection · chain A against A, TM-score 1.00
- P52895 · AlphaFold monomer V2.0 prediction for aldo-keto reductase family 1 member C2 (P52895) · 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 P52895
- Elsewhere: RCSB PDB 2IPJ · PDBe 2IPJ · UniProt P52895
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