Research workbench
Revisiting pH-gated conformational switch. complex HK853-RR468 pH 7
Analyse Revisiting pH-gated conformational switch. complex HK853-RR468 pH 7 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6RFV
- Type
- protein
- Length
- 706 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sensor histidine kinase; Response regulator
- UniProt
- Q9WZV7, Q9WYT9
- Ligands
- ADP, MG, SO4
- Pockets
- 5 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 46% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sensor histidine kinase | protein | 233 | 47% helix, 19% strand | Q9WZV7 |
| B | Sensor histidine kinase | protein | 232 | 48% helix, 20% strand | Q9WZV7 |
| C | Response regulator | protein | 120 | 43% helix, 19% strand | Q9WYT9 |
| D | Response regulator | protein | 121 | 43% helix, 19% strand | Q9WYT9 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains C, D
- SO4 · Sulfate ion · ion · 14 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 873 | 0.85 | 0.87 | 115 | ADP, SO4 |
| 2 | 770 | 0.85 | 0.88 | 98 | ADP, SO4, MG |
| 3 | 86 | 0.37 | 0.76 | 15 | empty |
| 4 | 61 | 0.32 | 0.76 | 12 | SO4 |
| 5 | 50 | 0.27 | 0.74 | 13 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1817 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 877 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 869 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 240 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 237 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide, 2 modified (disulfide, nonstandard).
Compared structures
- 6RFV · Revisiting pH-gated conformational switch. Complex HK853-RR468 pH 7 · 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 Q9WZV7
- Every structure of UniProt Q9WYT9
- Elsewhere: RCSB PDB 6RFV · PDBe 6RFV · UniProt Q9WZV7 · UniProt Q9WYT9
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