MolNFT v1 · #165560 · protein
Crystal structure of ketosteroid isomerase from pseudomonas putida (pksi) bound to 4-androstenedione at 280 K
6TZD · Steroid delta-isomerase: “Crystal structure of ketosteroid isomerase from pseudomonas putida (pksi) bound to 4-androstenedione at 280 K”. X-ray diffraction, 3 ligands (ASD, MG, CL), 3 pockets (best druggability 0.64). MolNFT v1…
- PDB
- 6TZD
- Type
- protein
- Length
- 252 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Steroid delta-isomerase
- EC
- 5.3.3.1
- UniProt
- P07445
- Ligands
- ASD, MG, CL
- Pockets
- 3 · best druggability 0.64
Structure
x-ray diffraction · 2 distinct chains · 29% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Steroid delta-isomerase (EC 5.3.3.1) | protein | 126 | 29% helix, 40% strand | P07445 |
| A | Steroid delta-isomerase (EC 5.3.3.1) | protein | 126 | 29% helix, 37% strand | P07445 |
Ligands and binding sites
- ASD · 4-androstene-3-17-dione · ligand · 2 copies · chains B, A
- MG · Magnesium ion · metal · chains A
- CL · Chloride ion · ion · 2 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 247 | 0.64 | 0.81 | 26 | ASD |
| 2 | 171 | 0.61 | 0.82 | 19 | ASD |
| 3 | 60 | 0.30 | 0.74 | 16 | empty |
Interfaces
1 interface between chains.
- B–A · 1094 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 6TZD · Crystal Structure of Ketosteroid Isomerase from Pseudomonas Putida (pKSI) bound to… · the same entry in another collection · chain B against B, TM-score 1.00
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 P07445
- Elsewhere: RCSB PDB 6TZD · PDBe 6TZD · UniProt P07445
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