Research workbench
Crystal structure of the sensor histidine kinase regulator yyci from bacillus subtitlis
Analyse Crystal structure of the sensor histidine kinase regulator yyci from bacillus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2O3O
- Type
- protein
- Length
- 2,871 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Yyci protein
- UniProt
- Q45612
- Ligands
- CL
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 11 distinct chains · 19% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Yyci protein | protein | 241 | 20% helix, 46% strand | Q45612 |
| B | Yyci protein | protein | 239 | 19% helix, 45% strand | Q45612 |
| C | Yyci protein | protein | 239 | 18% helix, 46% strand | Q45612 |
| D, H | Yyci protein | protein | 241 | 20% helix, 46% strand | Q45612 |
| E | Yyci protein | protein | 237 | 20% helix, 45% strand | Q45612 |
| F | Yyci protein | protein | 240 | 18% helix, 46% strand | Q45612 |
| G | Yyci protein | protein | 237 | 19% helix, 46% strand | Q45612 |
| I | Yyci protein | protein | 244 | 20% helix, 45% strand | Q45612 |
| J | Yyci protein | protein | 238 | 20% helix, 46% strand | Q45612 |
| K | Yyci protein | protein | 235 | 19% helix, 46% strand | Q45612 |
| L | Yyci protein | protein | 239 | 18% helix, 46% strand | Q45612 |
Ligands and binding sites
- CL · Chloride ion · ion · 6 copies · chains A, C, B, D, E, G, F, H, I, K, J, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 494 | 0.81 | 0.88 | 39 | CL |
| 2 | 497 | 0.80 | 0.87 | 39 | CL |
| 3 | 547 | 0.79 | 0.85 | 44 | CL |
| 4 | 725 | 0.78 | 0.83 | 77 | empty |
| 5 | 628 | 0.78 | 0.84 | 42 | CL |
Interfaces
22 interfaces between chains.
- F–H · 1879 Ų buried · 22 hydrogen bonds · protein-protein
- J–L · 1863 Ų buried · 25 hydrogen bonds · protein-protein
- B–D · 1857 Ų buried · 26 hydrogen bonds · protein-protein
- A–C · 1831 Ų buried · 25 hydrogen bonds · protein-protein
- I–K · 1704 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 72 modified (engineered).
Compared structures
- 2O3O · Crystal Structure of the sensor histidine kinase regulator YycI from Bacillus subtitlis · the same entry in another collection · chain L against L, 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 Q45612
- Elsewhere: RCSB PDB 2O3O · PDBe 2O3O · UniProt Q45612
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