Research workbench
Structure of yhda, K109D/D137K variant
Analyse Structure of yhda, K109D/D137K variant in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3GFS
- Type
- protein
- Length
- 2,003 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- FMN-dependent NADPH-azoreductase
- EC
- 1.7.-.-
- UniProt
- O07529
- Ligands
- FMN
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 45% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D, E, G, I, J, K | FMN-dependent NADPH-azoreductase (EC 1.7.-.-) | protein | 167 | 45% helix, 20% strand | O07529 |
| C | FMN-dependent NADPH-azoreductase (EC 1.7.-.-) | protein | 169 | 45% helix, 21% strand | O07529 |
| F, H, L | FMN-dependent NADPH-azoreductase (EC 1.7.-.-) | protein | 166 | 45% helix, 20% strand | O07529 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · 12 copies · chains A, C, B, D, E, F, G, H, I, J, K, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 250 | 0.82 | 0.95 | 35 | empty |
| 2 | 237 | 0.82 | 0.95 | 35 | empty |
| 3 | 146 | 0.77 | 0.95 | 36 | empty |
| 4 | 1086 | 0.75 | 0.78 | 67 | FMN |
| 5 | 489 | 0.64 | 0.76 | 58 | FMN |
Interfaces
23 interfaces between chains.
- K–L · 1165 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 1143 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 1142 Ų buried · 10 hydrogen bonds · protein-protein
- G–H · 1134 Ų buried · 10 hydrogen bonds · protein-protein
- E–F · 1120 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 3GFS · Structure of YhdA, K109D/D137K variant · the same entry in another collection · chain L against L, 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 O07529
- Elsewhere: RCSB PDB 3GFS · PDBe 3GFS · UniProt O07529
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