Research workbench
Crystal structure of ketosteroid isomerase P39GV40GS42G from pseudomonas testosteroni (tksi) bound to equilenin
Analyse Crystal structure of ketosteroid isomerase P39GV40GS42G from pseudomonas… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3OV4
- Type
- protein
- Length
- 485 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
- EQU, SO4
- Pockets
- 6 · best druggability 0.62
Structure
x-ray diffraction · 3 distinct chains · 30% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Steroid delta-isomerase (EC 5.3.3.1) | protein | 120 | 30% helix, 41% strand | P00947 |
| B | Steroid delta-isomerase (EC 5.3.3.1) | protein | 123 | 29% helix, 41% strand | P00947 |
| D | Steroid delta-isomerase (EC 5.3.3.1) | protein | 122 | 30% helix, 41% strand | P00947 |
Ligands and binding sites
- EQU · Equilenin · ligand · 3 copies · chains A, B, C
- SO4 · Sulfate ion · ion · 13 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 213 | 0.62 | 0.81 | 21 | EQU |
| 2 | 223 | 0.62 | 0.81 | 25 | empty |
| 3 | 206 | 0.61 | 0.81 | 22 | EQU |
| 4 | 166 | 0.60 | 0.82 | 20 | EQU |
| 5 | 79 | 0.58 | 0.88 | 22 | empty |
Interfaces
3 interfaces between chains.
- C–D · 968 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 932 Ų buried · 18 hydrogen bonds · protein-protein
- B–D · 387 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 3OV4 · Crystal Structure of Ketosteroid Isomerase P39GV40GS42G 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 0.98
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 3OV4 · PDBe 3OV4 · UniProt P00947
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