Research workbench
Crystal structure of the extracellular domain of the putative histidine kinase VPHK1S-Z8
Analyse Crystal structure of the extracellular domain of the putative histidine kinase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3LID
- Type
- protein
- Length
- 555 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative sensory BOX/GGDEF family protein
- UniProt
- Q87SR8
- Ligands
- PO4, CL
- Pockets
- 10 · best druggability 0.63
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative sensory BOX/GGDEF family protein | protein | 279 | 37% helix, 32% strand | Q87SR8 |
| B | Putative sensory BOX/GGDEF family protein | protein | 276 | 38% helix, 32% strand | Q87SR8 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 9 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 445 | 0.63 | 0.77 | 50 | EDO |
| 2 | 100 | 0.53 | 0.83 | 22 | EDO |
| 3 | 59 | 0.48 | 0.85 | 15 | empty |
| 4 | 184 | 0.46 | 0.75 | 28 | empty |
| 5 | 124 | 0.45 | 0.77 | 27 | empty |
Interfaces
1 interface between chains.
- A–B · 1341 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 3LID · Crystal Structure of the extracellular domain of the putative histidine kinase vpHK1S-Z8 · 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 Q87SR8
- Elsewhere: RCSB PDB 3LID · PDBe 3LID · UniProt Q87SR8
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