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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
- 1U55
- Type
- protein
- Length
- 375 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, CL
- Pockets
- 8 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Heme-based methyl-accepting chemotaxis protein | protein | 188 | 49% helix, 20% strand | Q8RBX6 |
| B | Heme-based methyl-accepting chemotaxis protein | protein | 187 | 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
- CL · Chloride ion · ion · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 317 | 0.85 | 0.94 | 36 | HEM, OXY |
| 2 | 290 | 0.83 | 0.94 | 36 | HEM, OXY |
| 3 | 161 | 0.45 | 0.75 | 33 | empty |
| 4 | 122 | 0.43 | 0.76 | 16 | empty |
| 5 | 122 | 0.43 | 0.76 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 775 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 1U55 · 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 1U55 · PDBe 1U55 · UniProt Q8RBX6
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