Research workbench
Crystal structure of ketosteroid isomerase D38ED99N from pseudomonas testosteroni (tksi)
Analyse Crystal structure of ketosteroid isomerase D38ED99N from pseudomonas… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3MKI
- Type
- protein
- Length
- 496 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
- SO4
- Pockets
- 7 · best druggability 0.75
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 | 124 | 29% helix, 40% strand | P00947 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 21 copies · chains A, B, D, C
- GOL · Glycerol · additive · 5 copies · chains B, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 90 | 0.75 | 0.96 | 20 | GOL |
| 2 | 255 | 0.73 | 0.87 | 40 | SO4, GOL |
| 3 | 125 | 0.56 | 0.82 | 18 | GOL |
| 4 | 95 | 0.56 | 0.85 | 21 | SO4 |
| 5 | 89 | 0.54 | 0.85 | 21 | SO4 |
Interfaces
3 interfaces between chains.
- C–D · 1138 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 1102 Ų buried · 19 hydrogen bonds · protein-protein
- B–D · 699 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 3MKI · Crystal Structure of Ketosteroid Isomerase D38ED99N from Pseudomonas Testosteroni (tKSI) · 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 0.99
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 P00947
- Elsewhere: RCSB PDB 3MKI · PDBe 3MKI · UniProt P00947
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