MolNFT v1 · #72118 · protein
Crystal structure of ketosteroid isomerase D38HD99N from pseudomonas testosteroni (tksi)
3MYT · Steroid delta-isomerase: “Crystal structure of ketosteroid isomerase D38HD99N from pseudomonas testosteroni (tksi)”. X-ray diffraction, 2 ligands (EQU, SO4), 7 pockets (best druggability 0.62). MolNFT v1 #72118 on GenesisL1: 3D…
- PDB
- 3MYT
- Type
- protein
- Length
- 498 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
- 7 · best druggability 0.62
Structure
x-ray diffraction · 2 distinct chains · 29% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Steroid delta-isomerase (EC 5.3.3.1) | protein | 124 | 29% helix, 40% strand | P00947 |
| B, C | Steroid delta-isomerase (EC 5.3.3.1) | protein | 125 | 28% helix, 41% strand | P00947 |
Ligands and binding sites
- EQU · Equilenin · ligand · 3 copies · chains A, B, C
- SO4 · Sulfate ion · ion · 15 copies · chains A, B, C, D
- GOL · Glycerol · additive · 4 copies · chains A, 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 | 138 | 0.62 | 0.84 | 18 | EQU |
| 2 | 177 | 0.62 | 0.82 | 22 | empty |
| 3 | 158 | 0.61 | 0.83 | 19 | empty |
| 4 | 91 | 0.59 | 0.87 | 18 | SO4 |
| 5 | 75 | 0.58 | 0.88 | 20 | SO4 |
Interfaces
4 interfaces between chains.
- B–D · 1084 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 1012 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 62 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 38 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 3MYT · Crystal structure of Ketosteroid Isomerase D38HD99N from Pseudomonas testosteroni (tKSI) · the same entry in another collection · chain C against C, 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 3MYT · PDBe 3MYT · UniProt P00947
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