Research workbench
Cryo-EM structure of dimeric quinol dependent nitric oxide reductase (qnor) from the pathogen neisseria meninigitidis
Analyse Cryo-EM structure of dimeric quinol dependent nitric oxide reductase (qnor)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6L3H
- Type
- protein
- Length
- 1,482 residues
- Chains
- 2
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nitric-oxide reductase
- EC
- 1.7.99.7
- UniProt
- C6S880
- Ligands
- HEM, FE, CA
- Pockets
- 20 · best druggability 0.90
Structure
electron microscopy · 1 distinct chain · 61% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Nitric-oxide reductase (EC 1.7.99.7) | protein | 741 | 61% helix, 3% strand | C6S880 |
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
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1074 | 0.90 | 0.91 | 112 | HEM |
| 2 | 1024 | 0.89 | 0.91 | 104 | HEM, CA |
| 3 | 1182 | 0.86 | 0.87 | 103 | empty |
| 4 | 91 | 0.77 | 0.97 | 20 | empty |
| 5 | 76 | 0.73 | 0.96 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 2254 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 6L3H · Cryo-EM structure of dimeric quinol dependent Nitric Oxide Reductase (qNOR) from the… · 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 C6S880
- Elsewhere: RCSB PDB 6L3H · PDBe 6L3H · UniProt C6S880
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