MolNFT v1 · #161821 · protein
Cryo-EM structure of dimeric quinol dependent nitric oxide reductase (qnor) from alcaligenes xylosoxidans
6QQ5 · Nitric oxide reductase subunit B: “Cryo-EM structure of dimeric quinol dependent nitric oxide reductase (qnor) from alcaligenes xylosoxidans”. Electron microscopy, 3 ligands (HEM, FE, CA), 16 pockets (best druggability 0.88). MolNFT…
- PDB
- 6QQ5
- Type
- protein
- Length
- 1,476 residues
- Chains
- 2
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nitric oxide reductase subunit B
- EC
- 1.7.2.5
- UniProt
- A0A0D6H8R3
- Ligands
- HEM, FE, CA
- Pockets
- 16 · best druggability 0.88
Structure
electron microscopy · 1 distinct chain · 54% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Nitric oxide reductase subunit B (EC 1.7.2.5) | protein | 738 | 54% helix, 2% strand | A0A0D6H8R3 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B
- FE · Fe (III) ion · metal · 2 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 909 | 0.88 | 0.90 | 84 | HEM |
| 2 | 881 | 0.88 | 0.90 | 82 | HEM, CA |
| 3 | 1071 | 0.83 | 0.84 | 87 | empty |
| 4 | 893 | 0.76 | 0.79 | 77 | empty |
| 5 | 103 | 0.49 | 0.80 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 2176 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6QQ5 · Cryo-EM structure of dimeric quinol dependent nitric oxide reductase (qNOR) from… · 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 A0A0D6H8R3
- Elsewhere: RCSB PDB 6QQ5 · PDBe 6QQ5 · UniProt A0A0D6H8R3
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.