MolNFT v1 · #162709 · protein
Revisiting pH-gated conformational switch. complex HK853-RR468 pH 7.5
6RGY · Osmosensitive K+ channel histidine kinase kdpd: “Revisiting pH-gated conformational switch. complex HK853-RR468 pH 7.5”. X-ray diffraction, 3 ligands (ADP, MG, SO4), 5 pockets (best druggability 0.84). MolNFT v1 #162709 on…
- PDB
- 6RGY
- Type
- protein
- Length
- 713 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Osmosensitive K+ channel histidine kinase kdpd; Response regulator
- EC
- 2.7.3.-
- UniProt
- R4NPW0, Q9WYT9
- Ligands
- ADP, MG, SO4
- Pockets
- 5 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 46% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Osmosensitive K+ channel histidine kinase kdpd (EC 2.7.3.-) | protein | 236 | 47% helix, 19% strand | R4NPW0 |
| B | Osmosensitive K+ channel histidine kinase kdpd (EC 2.7.3.-) | protein | 236 | 50% helix, 20% strand | R4NPW0 |
| C | Response regulator | protein | 120 | 43% helix, 19% strand | Q9WYT9 |
| D | Response regulator | protein | 121 | 41% 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 · 13 copies · chains A, B, C, D
- CIT · Citric acid · additive · chains B, 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 | 933 | 0.84 | 0.85 | 112 | ADP, SO4 |
| 2 | 935 | 0.84 | 0.85 | 115 | ADP, SO4 |
| 3 | 86 | 0.37 | 0.76 | 17 | SO4 |
| 4 | 51 | 0.36 | 0.80 | 13 | empty |
| 5 | 88 | 0.36 | 0.75 | 18 | SO4 |
Interfaces
5 interfaces between chains.
- A–B · 1888 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 956 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 894 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 275 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 268 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide, 2 modified (disulfide, nonstandard).
Compared structures
- 6RGY · Revisiting pH-gated conformational switch. Complex HK853-RR468 pH 7.5 · 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 R4NPW0
- Every structure of UniProt Q9WYT9
- Elsewhere: RCSB PDB 6RGY · PDBe 6RGY · UniProt R4NPW0 · UniProt Q9WYT9
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