Research workbench
Crystal structure of an oxygen binding H-nox domain related to soluble guanylate cyclases (oxygen complex)
Analyse Crystal structure of an oxygen binding H-nox domain related to soluble… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1U4H
- Type
- protein
- Length
- 376 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Heme-based methyl-accepting chemotaxis protein
- UniProt
- Q8RBX6
- Ligands
- HEM, OXY, SCN
- Pockets
- 4 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 48% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Heme-based methyl-accepting chemotaxis protein | protein | 188 | 48% helix, 20% strand | Q8RBX6 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- OXY · Oxygen molecule · ion · 2 copies · chains A, B
- SCN · Thiocyanate ion · ion · chains B
- GOL · Glycerol · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 323 | 0.82 | 0.92 | 38 | HEM, OXY, GOL |
| 2 | 305 | 0.82 | 0.92 | 37 | SCN, HEM, OXY |
| 3 | 165 | 0.41 | 0.73 | 25 | empty |
| 4 | 70 | 0.33 | 0.75 | 16 | GOL |
Interfaces
1 interface between chains.
- A–B · 321 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 modified (engineered).
Compared structures
- 1U4H · Crystal structure of an oxygen binding H-NOX domain related to soluble guanylate cyclases… · 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 Q8RBX6
- Elsewhere: RCSB PDB 1U4H · PDBe 1U4H · UniProt Q8RBX6
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