Research workbench
X-ray structure of the heme-bound gaf domain of sensory histidine kinase dost of mycobacterium tuberculosis
Analyse X-ray structure of the heme-bound gaf domain of sensory histidine kinase dost… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2VZW
- Type
- protein
- Length
- 295 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable histidine kinase response regulator
- UniProt
- O53473
- Ligands
- HEM, OXY
- Pockets
- 5 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Probable histidine kinase response regulator | protein | 146 | 36% helix, 26% strand | O53473 |
| B | Probable histidine kinase response regulator | protein | 149 | 37% helix, 26% strand | O53473 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- OXY · Oxygen molecule · ion · chains B
- ACT · Acetate ion · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 312 | 0.80 | 0.90 | 34 | HEM, OXY |
| 2 | 329 | 0.78 | 0.88 | 43 | HEM |
| 3 | 177 | 0.50 | 0.77 | 22 | empty |
| 4 | 142 | 0.41 | 0.74 | 29 | empty |
| 5 | 94 | 0.38 | 0.76 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 672 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 2VZW · X-ray structure of the heme-bound GAF domain of sensory histidine kinase DosT of… · 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 O53473
- Elsewhere: RCSB PDB 2VZW · PDBe 2VZW · UniProt O53473
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