Research workbench
Crystal structure of the putative NADPH-dependent azobenzene FMN- reductase yhda from bacillus subtilis, northeast structural genomics target SR135
Analyse Crystal structure of the putative NADPH-dependent azobenzene FMN- reductase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2GSW
- Type
- protein
- Length
- 672 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Yhda
- Ligands
- FMN
- Pockets
- 8 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Yhda | protein | 168 | 45% helix, 18% strand | — |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · 4 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 327 | 0.84 | 0.94 | 44 | empty |
| 2 | 101 | 0.53 | 0.83 | 14 | empty |
| 3 | 60 | 0.51 | 0.85 | 14 | empty |
| 4 | 257 | 0.50 | 0.74 | 39 | FMN |
| 5 | 173 | 0.45 | 0.75 | 29 | FMN |
Interfaces
6 interfaces between chains.
- A–C · 1129 Ų buried · 13 hydrogen bonds · protein-protein
- B–D · 1061 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 780 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 674 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 354 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 modified (engineered).
Compared structures
- 2GSW · Crystal Structure of the Putative NADPH-dependent Azobenzene FMN-Reductase YhdA 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
- Elsewhere: RCSB PDB 2GSW · PDBe 2GSW
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.