MolNFT v1 · #107412 · protein
Crystal structure of an H-nox protein from S. oneidensis in the MN(II)NO ligation state, Q154A/Q155A/K156A mutant
4U9K · No-binding heme-dependent sensor protein: “Crystal structure of an H-nox protein from S. oneidensis in the MN(II)NO ligation state, Q154A/Q155A/K156A…”. X-ray diffraction, 4 ligands (MNH, ZN, NA), 5 pockets (best druggability 0.84).…
- PDB
- 4U9K
- Type
- protein
- Length
- 373 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- No-binding heme-dependent sensor protein
- UniProt
- Q8EF49
- Ligands
- MNH, ZN, NA, NO
- Pockets
- 5 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 52% 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, 13% 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
- NO · Nitric oxide · ion · 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 | 422 | 0.84 | 0.91 | 52 | MNH |
| 2 | 889 | 0.84 | 0.86 | 75 | MNH, NO |
| 3 | 140 | 0.49 | 0.78 | 23 | empty |
| 4 | 55 | 0.47 | 0.84 | 12 | empty |
| 5 | 92 | 0.45 | 0.80 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 615 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 4U9K · Crystal structure of an H-NOX protein from S. oneidensis in the Mn(II)NO 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 4U9K · PDBe 4U9K · UniProt Q8EF49
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