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The crystal structure of FMN-dependent NADH-azoreductase 1 (GBAA0966) from bacillus anthracis str. ames ancestor
Analyse The crystal structure of FMN-dependent NADH-azoreductase 1 (GBAA0966) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3U7I
- Type
- protein
- Length
- 876 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- FMN-dependent NADH-azoreductase 1
- EC
- 1.7.-.-
- UniProt
- Q81UB2
- Ligands
- CL
- Pockets
- 4 · best druggability 0.71
Structure
x-ray diffraction · 4 distinct chains · 42% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | FMN-dependent NADH-azoreductase 1 (EC 1.7.-.-) | protein | 218 | 42% helix, 19% strand | Q81UB2 |
| B | FMN-dependent NADH-azoreductase 1 (EC 1.7.-.-) | protein | 220 | 43% helix, 20% strand | Q81UB2 |
| C | FMN-dependent NADH-azoreductase 1 (EC 1.7.-.-) | protein | 220 | 42% helix, 19% strand | Q81UB2 |
| D | FMN-dependent NADH-azoreductase 1 (EC 1.7.-.-) | protein | 218 | 43% helix, 20% strand | Q81UB2 |
Ligands and binding sites
- CL · Chloride ion · ion · 7 copies · chains A, B, C, D
- GOL · Glycerol · additive · 4 copies · chains A, B, D
- PEG · Di(hydroxyethyl)ether · additive · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 872 | 0.71 | 0.76 | 84 | CL, GOL |
| 2 | 546 | 0.68 | 0.78 | 51 | CL |
| 3 | 557 | 0.66 | 0.76 | 46 | CL, GOL |
| 4 | 512 | 0.64 | 0.76 | 47 | CL, GOL |
Interfaces
5 interfaces between chains.
- A–C · 1515 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 1453 Ų buried · 14 hydrogen bonds · protein-protein
- A–D · 167 Ų buried · 1 hydrogen bond · protein-protein
- A–B · 61 Ų buried · 1 hydrogen bond · protein-protein
- C–D · 52 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 27 modified (engineered).
Compared structures
- 3U7I · The crystal structure of FMN-dependent NADH-azoreductase 1 (GBAA0966) from Bacillus… · the same entry in another collection · chain D against D, TM-score 1.00
- Q81UB2 · AlphaFold monomer V2.0 prediction for FMN-dependent NADH:QUINONE oxidoreductase 1 (Q81UB2) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 Q81UB2
- Elsewhere: RCSB PDB 3U7I · PDBe 3U7I · UniProt Q81UB2
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