MolNFT v2 · #218106 · protein
Structure of WT SpNox DH domain: a bacterial NADPH oxidase.
8QQ5 · Oxidoreductase: “Structure of WT SpNox DH domain: a bacterial NADPH oxidase.”. X-ray diffraction at 2.5, 2 ligands (FAD, CL), 10 pockets (best druggability 0.73). MolNFT v2 #218106 on GenesisL1: 3D structure, binding sites and…
- PDB
- 8QQ5
- Type
- protein
- Length
- 654 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.5
- Source
- Streptococcus pneumoniae
- Molecule
- Oxidoreductase
- UniProt
- A0A4J2B4U9
- Ligands
- FAD, CL
- Pockets
- 10 · best druggability 0.73
Structure
x-ray diffraction · resolution 2.5 · 3 distinct chains · 25% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Oxidoreductase | protein | 221 | 24% helix, 37% strand | A0A4J2B4U9 |
| B | Oxidoreductase | protein | 219 | 24% helix, 37% strand | A0A4J2B4U9 |
| C | Oxidoreductase | protein | 214 | 26% helix, 39% strand | A0A4J2B4U9 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B, C
- CL · Chloride ion · ion · 2 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 560 | 0.73 | 0.81 | 58 | empty |
| 2 | 175 | 0.57 | 0.81 | 23 | FAD |
| 3 | 174 | 0.56 | 0.80 | 22 | FAD |
| 4 | 201 | 0.56 | 0.79 | 23 | empty |
| 5 | 108 | 0.52 | 0.82 | 24 | empty |
Interfaces
2 interfaces between chains.
- B–C · 1025 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 225 Ų buried · 3 hydrogen bonds · protein-protein
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 A0A4J2B4U9
- Elsewhere: RCSB PDB 8QQ5 · PDBe 8QQ5 · UniProt A0A4J2B4U9
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