Research workbench
Crystal structure of human type 3 3ALPHA-hydroxysteroid dehydrogenase in complex with NADP(H)
Analyse Crystal structure of human type 3 3ALPHA-hydroxysteroid dehydrogenase in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2HDJ
- Type
- protein
- Length
- 644 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
- NDP, SO4
- Pockets
- 9 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 16% 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 | 322 | 39% helix, 16% strand | P52895 |
Ligands and binding sites
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 665 | 0.82 | 0.87 | 60 | empty |
| 2 | 435 | 0.77 | 0.85 | 48 | NDP, EDO |
| 3 | 418 | 0.76 | 0.85 | 48 | NDP, EDO |
| 4 | 150 | 0.51 | 0.79 | 25 | EDO |
| 5 | 90 | 0.50 | 0.82 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 1239 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 2HDJ · Crystal structure of human type 3 3alpha-hydroxysteroid dehydrogenase in complex with… · the same entry in another collection · chain B against B, 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 2HDJ · PDBe 2HDJ · UniProt P52895
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