Research workbench
Crystal structure of 5-3-ketosteroid isomerase mutant D38N from pseudomonas testosteroni complexed with 5ALPHA-estran-3,17-dione
Analyse Crystal structure of 5-3-ketosteroid isomerase mutant D38N from pseudomonas… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1OHP
- Type
- protein
- Length
- 500 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Steroid delta-isomerase
- EC
- 5.3.3.1
- UniProt
- P00947
- Ligands
- ESR
- Pockets
- 5 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 29% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Steroid delta-isomerase (EC 5.3.3.1) | protein | 125 | 29% helix, 40% strand | P00947 |
Ligands and binding sites
- ESR · 5-alpha-estran-3,17-dione · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 522 | 0.78 | 0.85 | 76 | empty |
| 2 | 166 | 0.62 | 0.83 | 21 | ESR |
| 3 | 178 | 0.59 | 0.81 | 20 | ESR |
| 4 | 198 | 0.59 | 0.80 | 22 | ESR |
| 5 | 200 | 0.59 | 0.80 | 23 | ESR |
Interfaces
4 interfaces between chains.
- C–D · 1100 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1076 Ų buried · 19 hydrogen bonds · protein-protein
- B–D · 567 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 195 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 1OHP · Crystal structure of 5-3-ketosteroid isomerase mutant D38N from pseudomonas testosteroni… · the same entry in another collection · chain A against A, TM-score 1.00
- P00947 · AlphaFold monomer V2.0 prediction for steroid delta-isomerase (P00947) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 P00947
- Elsewhere: RCSB PDB 1OHP · PDBe 1OHP · UniProt P00947
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