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Crystal structure of nitric oxide reductase complex with HQNO
Analyse Crystal structure of nitric oxide reductase complex with HQNO in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3AYG
- Type
- protein
- Length
- 754 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.7
- Source
- Geobacillus stearothermophilus
- Molecule
- Nitric oxide reductase
- UniProt
- B3Y963
- Ligands
- HEM, LOP, HQO, ZN, CA
- Pockets
- 8 · best druggability 0.88
Structure
x-ray diffraction · resolution 2.7 · 1 distinct chain · 70% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nitric oxide reductase | protein | 754 | 70% helix, 4% strand | B3Y963 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A
- LOP · (1R)-2-{[(R)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-1-[(dodecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate · ligand · 2 copies · chains A
- HQO · 2-heptyl-4-hydroxy quinoline N-oxide · ligand · chains A
- ZN · Zinc ion · metal · chains A
- CA · Calcium ion · metal · chains A
- BOG · octyl beta-D-glucopyranoside · additive · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1116 | 0.88 | 0.89 | 120 | HEM, ZN, CA, HQO |
| 2 | 243 | 0.82 | 0.94 | 30 | empty |
| 3 | 76 | 0.55 | 0.86 | 17 | empty |
| 4 | 201 | 0.51 | 0.76 | 25 | BOG |
| 5 | 132 | 0.48 | 0.78 | 21 | empty |
Compared structures
- 3AYG · Crystal structure of nitric oxide reductase complex with hqno · 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 B3Y963
- Elsewhere: RCSB PDB 3AYG · PDBe 3AYG · UniProt B3Y963
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