Research workbench
Crystal structure of ketosteroid isomerase from pseudomonas putida (pksi) bound to equilenin; D40N, Y16(CL-Y)
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
- 5KP1
- Type
- protein
- Length
- 501 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
- P07445
- Ligands
- EQU, SO4
- Pockets
- 6 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | Steroid delta-isomerase (EC 5.3.3.1) | protein | 125 | 31% helix, 40% strand | P07445 |
| C | Steroid delta-isomerase (EC 5.3.3.1) | protein | 126 | 32% helix, 40% strand | P07445 |
Ligands and binding sites
- EQU · Equilenin · ligand · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 2 copies · chains A, 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 959 | 0.81 | 0.83 | 101 | empty |
| 2 | 198 | 0.63 | 0.82 | 21 | EQU |
| 3 | 184 | 0.62 | 0.82 | 24 | EQU |
| 4 | 217 | 0.62 | 0.81 | 28 | EQU |
| 5 | 193 | 0.61 | 0.82 | 26 | EQU |
Interfaces
5 interfaces between chains.
- C–D · 1091 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 1090 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 364 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 223 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 220 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (nonstandard).
Compared structures
- 5KP1 · 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 5KP1 · PDBe 5KP1 · UniProt P07445
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