Research workbench
Crystal structure of FE(II) no-bound H-nox protein from C. subterraneus
Analyse Crystal structure of FE(II) no-bound H-nox protein from C. subterraneus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5JRV
- Type
- protein
- Length
- 376 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Methyl-accepting chemotaxis protein
- UniProt
- Q8RBX6
- Ligands
- HEM, NO, IOD
- Pockets
- 7 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 49% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Methyl-accepting chemotaxis protein | protein | 188 | 49% helix, 21% strand | Q8RBX6 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- NO · Nitric oxide · ion · 2 copies · chains A, B
- IOD · Iodide ion · ion · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 333 | 0.85 | 0.94 | 46 | HEM, NO, IOD |
| 2 | 319 | 0.83 | 0.93 | 37 | HEM, NO |
| 3 | 277 | 0.53 | 0.75 | 28 | empty |
| 4 | 168 | 0.50 | 0.77 | 21 | empty |
| 5 | 102 | 0.43 | 0.78 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 636 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 1 cofactor (heme attachment).
Compared structures
- 5JRV · Crystal structure of Fe(II) NO-bound H-NOX protein from C. subterraneus · 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 5JRV · PDBe 5JRV · UniProt Q8RBX6
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