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Crystal structure of an H-NOX protein from S. oneidensis in the Mn(II) ligation state, Q154A/Q155A/K156A mutant
Analyse Crystal structure of an H-NOX protein from S. oneidensis in the Mn(II) ligation… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4U9J
- Type
- protein
- Length
- 373 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.1
- Source
- Shewanella oneidensis
- Molecule
- NO-binding heme-dependent sensor protein
- UniProt
- Q8EF49
- Ligands
- MNH, ZN, NA
- Pockets
- 5 · best druggability 0.85
Structure
x-ray diffraction · resolution 2.1 · 2 distinct chains · 53% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NO-binding heme-dependent sensor protein | protein | 187 | 52% helix, 18% strand | Q8EF49 |
| B | NO-binding heme-dependent sensor protein | protein | 186 | 53% helix, 15% strand | Q8EF49 |
Ligands and binding sites
- MNH · Manganese protoporphyrin IX · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- NA · Sodium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 445 | 0.85 | 0.91 | 51 | MNH |
| 2 | 870 | 0.84 | 0.86 | 75 | MNH |
| 3 | 120 | 0.48 | 0.79 | 22 | empty |
| 4 | 94 | 0.48 | 0.82 | 18 | empty |
| 5 | 56 | 0.46 | 0.83 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 604 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 4U9J · Crystal structure of an H-nox protein from S. oneidensis in the MN(II) ligation state… · 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 Q8EF49
- Elsewhere: RCSB PDB 4U9J · PDBe 4U9J · UniProt Q8EF49
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