MolNFT v1 · #179616 · protein
The structure of a sensor domain of a histidine kinase (vxra) from vibrio cholerae O1 biovar eltor str. N16961, 2ND form
7KB3 · Sensor histidine kinase: “The structure of a sensor domain of a histidine kinase (vxra) from vibrio cholerae O1 biovar eltor str.…”. X-ray diffraction, 2 ligands (SRT, CL), 11 pockets (best druggability 0.84). MolNFT v1 #179616 on…
- PDB
- 7KB3
- Type
- protein
- Length
- 872 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sensor histidine kinase
- UniProt
- Q9KM24
- Ligands
- SRT, CL
- Pockets
- 11 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 46% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sensor histidine kinase | protein | 219 | 46% helix, 15% strand | Q9KM24 |
| B | Sensor histidine kinase | protein | 216 | 45% helix, 16% strand | Q9KM24 |
| C | Sensor histidine kinase | protein | 217 | 47% helix, 16% strand | Q9KM24 |
| D | Sensor histidine kinase | protein | 220 | 46% helix, 15% strand | Q9KM24 |
Ligands and binding sites
- SRT · S,R meso-tartaric acid · ligand · chains A, B, C
- CL · Chloride ion · ion · 21 copies · chains A, B, C, D
- ACT · Acetate ion · additive · 9 copies · chains A, D, B, C
- GOL · Glycerol · additive · 4 copies · chains A, B, D
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1171 | 0.84 | 0.85 | 127 | ACT, GOL |
| 2 | 262 | 0.59 | 0.79 | 29 | CL |
| 3 | 225 | 0.57 | 0.79 | 28 | CL |
| 4 | 85 | 0.54 | 0.85 | 17 | empty |
| 5 | 194 | 0.54 | 0.78 | 24 | empty |
Interfaces
6 interfaces between chains.
- B–D · 1667 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 1617 Ų buried · 24 hydrogen bonds · protein-protein
- A–C · 1581 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 1562 Ų buried · 21 hydrogen bonds · protein-protein
- A–D · 848 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 1 covalent (disulfide, additive adduct).
Compared structures
- 7KB3 · The structure of a sensor domain of a histidine kinase (VxrA) from Vibrio cholerae O1… · 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 Q9KM24
- Elsewhere: RCSB PDB 7KB3 · PDBe 7KB3 · UniProt Q9KM24
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