Research workbench
Crystal structure of ketosteroid isomerase from pseudomonas putida (pksi) bound to 19-nortestosterone
Analyse Crystal structure of ketosteroid isomerase from pseudomonas putida (pksi) bound… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5KP4
- Type
- protein
- Length
- 254 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
- 6VW
- Pockets
- 3 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 30% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Steroid delta-isomerase (EC 5.3.3.1) | protein | 127 | 31% helix, 38% strand | P07445 |
| B | Steroid delta-isomerase (EC 5.3.3.1) | protein | 127 | 29% helix, 40% strand | P07445 |
Ligands and binding sites
- 6VW · (8~{R},9~{S},10~{R},13~{S},14~{S},17~{S})-13-methyl-17-oxidanyl-2,6,7,8,9,10,11,12,14,15,16,17-dodecahydro-1~{H}-cyclopenta[a]phenanthren-3-one · ligand · chains B
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 | 242 | 0.65 | 0.82 | 28 | empty |
| 2 | 220 | 0.63 | 0.81 | 25 | 6VW |
| 3 | 79 | 0.32 | 0.74 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1080 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 5KP4 · Crystal Structure of Ketosteroid Isomerase from Pseudomonas putida (pKSI) bound to… · the same entry in another collection · chain A against A, 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 5KP4 · PDBe 5KP4 · UniProt P07445
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