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Crystal Structure of Ketosteroid Isomerase D38N mutant from Mycobacterium hassiacum (mhKSI) bound to 3,4-dinitrophenol
Analyse Crystal Structure of Ketosteroid Isomerase D38N mutant from Mycobacterium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6P44
- Type
- protein
- Length
- 232 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.251
- Source
- Mycobacterium hassiacum (strain DSM 44199 / CIP 105218 / JCM 12690 / 3849)
- Molecule
- SnoaL-like domain protein
- EC
- 5.3.3.1
- UniProt
- K5BJ73
- Ligands
- DNX, GAI, SO4
- Pockets
- 3 · best druggability 0.54
Structure
x-ray diffraction · resolution 1.251 · 2 distinct chains · 31% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SnoaL-like domain protein (EC 5.3.3.1) | protein | 115 | 30% helix, 40% strand | K5BJ73 |
| B | SnoaL-like domain protein (EC 5.3.3.1) | protein | 117 | 32% helix, 43% strand | K5BJ73 |
Ligands and binding sites
- DNX · 3,4-dinitrophenol · ligand · 2 copies · chains A, B
- GAI · Guanidine · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 116 | 0.54 | 0.82 | 22 | DNX |
| 2 | 158 | 0.50 | 0.77 | 22 | DNX |
| 3 | 82 | 0.42 | 0.79 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 882 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 6P44 · Crystal structure of ketosteroid isomerase D38N mutant from mycobacterium hassiacum… · 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 K5BJ73
- Elsewhere: RCSB PDB 6P44 · PDBe 6P44 · UniProt K5BJ73
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