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Structural genomics, the crystal structure of the C- terminal domain of yurk from bacillus subtilis subsp. subtilis str. 168
Analyse Structural genomics, the crystal structure of the C- terminal domain of yurk… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2IKK
- Type
- protein
- Length
- 291 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hypothetical transcriptional regulator yurk
- UniProt
- O32152
- Ligands
- SO4
- Pockets
- 3 · best druggability 0.45
Structure
x-ray diffraction · 2 distinct chains · 21% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hypothetical transcriptional regulator yurk | protein | 146 | 21% helix, 48% strand | O32152 |
| B | Hypothetical transcriptional regulator yurk | protein | 145 | 21% helix, 47% strand | O32152 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 2 copies · chains A, 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, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 125 | 0.45 | 0.76 | 17 | empty |
| 2 | 103 | 0.43 | 0.77 | 23 | SO4 |
| 3 | 52 | 0.29 | 0.76 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 882 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (engineered).
Compared structures
- 2IKK · Structural Genomics, the crystal structure of the C-terminal domain of Yurk from Bacillus… · the same entry in another collection · chain A against A, TM-score 1.00
- O32152 · AlphaFold monomer V2.0 prediction for uncharacterized hth-type transcriptional regulator… · a predicted model of the same protein · chain B against A, TM-score 0.95
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 O32152
- Elsewhere: RCSB PDB 2IKK · PDBe 2IKK · UniProt O32152
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