MolNFT v1 · #64858 · protein
Structure of yhda, D137L variant
3GFR · FMN-dependent NADPH-azoreductase: “Structure of yhda, D137L variant”. X-ray diffraction, 1 ligand (FMN), 8 pockets (best druggability 0.61). MolNFT v1 #64858 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3GFR
- Type
- protein
- Length
- 673 residues
- Chains
- 4
- 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
- 8 · best druggability 0.61
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | FMN-dependent NADPH-azoreductase (EC 1.7.-.-) | protein | 167 | 46% helix, 20% strand | O07529 |
| D | FMN-dependent NADPH-azoreductase (EC 1.7.-.-) | protein | 172 | 43% helix, 21% strand | O07529 |
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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 259 | 0.61 | 0.80 | 33 | empty |
| 2 | 258 | 0.60 | 0.79 | 30 | empty |
| 3 | 170 | 0.48 | 0.77 | 31 | empty |
| 4 | 71 | 0.43 | 0.81 | 16 | empty |
| 5 | 112 | 0.39 | 0.75 | 17 | empty |
Interfaces
5 interfaces between chains.
- B–D · 1127 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 1117 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 585 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 331 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 306 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
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 3GFR · PDBe 3GFR · UniProt O07529
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