MolNFT v1 · #162710 · protein
Revisiting pH-gated conformational switch. complex HK853-RR468 pH 6.5
6RGZ · Sensor histidine kinase: “Revisiting pH-gated conformational switch. complex HK853-RR468 pH 6.5”. X-ray diffraction, 4 ligands (ADP, MG, SO4), 4 pockets (best druggability 0.84). MolNFT v1 #162710 on GenesisL1: 3D structure, binding…
- PDB
- 6RGZ
- Type
- protein
- Length
- 713 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, CL
- Pockets
- 4 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 47% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sensor histidine kinase | protein | 237 | 50% helix, 19% strand | Q9WZV7 |
| B | Sensor histidine kinase | protein | 233 | 50% helix, 20% strand | Q9WZV7 |
| C | Response regulator | protein | 121 | 41% helix, 19% strand | Q9WYT9 |
| D | Response regulator | protein | 122 | 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, D, C
- CL · Chloride ion · ion · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 990 | 0.84 | 0.85 | 112 | ADP, SO4 |
| 2 | 945 | 0.84 | 0.85 | 98 | ADP, SO4 |
| 3 | 63 | 0.31 | 0.75 | 12 | SO4 |
| 4 | 52 | 0.30 | 0.77 | 15 | SO4 |
Interfaces
5 interfaces between chains.
- A–B · 1885 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 874 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 864 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 267 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 264 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide, 2 modified (disulfide, nonstandard).
Compared structures
- 6RGZ · Revisiting pH-gated conformational switch. Complex HK853-RR468 pH 6.5 · 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 6RGZ · PDBe 6RGZ · UniProt Q9WZV7 · UniProt Q9WYT9
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