MolNFT v1 · #59446 · protein
Crystal structure of the V. cholerae histidine kinase dctb sensor domain
3BY9 · Sensor protein: “Crystal structure of the V. cholerae histidine kinase dctb sensor domain”. X-ray diffraction, 1 ligand (CA), 2 pockets (best druggability 0.31). MolNFT v1 #59446 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 3BY9
- Type
- protein
- Length
- 517 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sensor protein
- EC
- 2.7.13.3
- UniProt
- Q9KQS3
- Ligands
- CA
- Pockets
- 2 · best druggability 0.31
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sensor protein (EC 2.7.13.3) | protein | 259 | 33% helix, 28% strand | Q9KQS3 |
| B | Sensor protein (EC 2.7.13.3) | protein | 258 | 30% helix, 28% strand | Q9KQS3 |
Ligands and binding sites
- CA · Calcium ion · metal · 2 copies · chains A
- SIN · Succinic acid · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 72 | 0.31 | 0.74 | 15 | empty |
| 2 | 55 | 0.29 | 0.75 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 70 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 modified (engineered).
Compared structures
- 3BY9 · Crystal structure of the V. cholerae Histidine Kinase DctB Sensor Domain · 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 Q9KQS3
- Elsewhere: RCSB PDB 3BY9 · PDBe 3BY9 · UniProt Q9KQS3
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