Research workbench
Globin sensor domain of afgchk (feiii form) in complex with cyanide
Analyse Globin sensor domain of afgchk (feiii form) in complex with cyanide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5OHE
- Type
- protein
- Length
- 1,218 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Globin-coupled histidine kinase
- EC
- 2.7.13.3
- UniProt
- A7HD43
- Ligands
- HEM, NA, CYN, CL
- Pockets
- 17 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 82% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D, E, G, H | Globin-coupled histidine kinase (EC 2.7.13.3) | protein | 152 | 84% helix, 0% strand | A7HD43 |
| C | Globin-coupled histidine kinase (EC 2.7.13.3) | protein | 151 | 81% helix, 0% strand | A7HD43 |
| F | Globin-coupled histidine kinase (EC 2.7.13.3) | protein | 155 | 81% helix, 0% strand | A7HD43 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- NA · Sodium ion · metal · chains E
- CYN · Cyanide ion · ion · 6 copies · chains A, B, C, E, G, H
- CL · Chloride ion · ion · 4 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 111 | 0.79 | 0.98 | 24 | CL |
| 2 | 108 | 0.78 | 0.98 | 26 | CL |
| 3 | 114 | 0.78 | 0.97 | 26 | CL |
| 4 | 100 | 0.78 | 0.98 | 27 | CL |
| 5 | 1196 | 0.74 | 0.77 | 92 | empty |
Interfaces
13 interfaces between chains.
- E–F · 1933 Ų buried · 31 hydrogen bonds · protein-protein
- C–D · 1903 Ų buried · 29 hydrogen bonds · protein-protein
- G–H · 1880 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 1847 Ų buried · 31 hydrogen bonds · protein-protein
- A–H · 479 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 5OHE · Globin sensor domain of AfGcHK (FeIII form) in complex with cyanide · the same entry in another collection · chain H against H, TM-score 1.00
- A7HD43 · AlphaFold monomer V2.0 prediction for globin-coupled histidine kinase (A7HD43) · a predicted model of the same protein · chain E against A, TM-score 0.99
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 A7HD43
- Elsewhere: RCSB PDB 5OHE · PDBe 5OHE · UniProt A7HD43
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