MolNFT v1 · #64803 · protein
Crystal structure of a putative NAD(P)H:FMN oxidoreductase (PG0310) from porphyromonas gingivalis W83 at 1.70 a resolution
3GE5: “Crystal structure of a putative NAD(P)H:FMN oxidoreductase (PG0310) from porphyromonas gingivalis W83 at 1.70…”. X-ray diffraction, 3 ligands (FMN, UNL, SO4), 6 pockets (best druggability 0.70). MolNFT v1 #64803 on GenesisL1: 3D…
- PDB
- 3GE5
- Type
- protein
- Length
- 351 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative NAD(P)H:FMN oxidoreductase
- UniProt
- Q7MX99
- Ligands
- FMN, UNL, SO4
- Pockets
- 6 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative NAD(P)H:FMN oxidoreductase | protein | 176 | 36% helix, 22% strand | Q7MX99 |
| B | Putative NAD(P)H:FMN oxidoreductase | protein | 175 | 37% helix, 22% strand | Q7MX99 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · 2 copies · chains A, B
- UNL · Unknown ligand · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 3 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 215 | 0.70 | 0.87 | 28 | UNL, FMN |
| 2 | 231 | 0.68 | 0.85 | 29 | FMN, UNL |
| 3 | 107 | 0.37 | 0.75 | 27 | EDO |
| 4 | 85 | 0.36 | 0.76 | 22 | empty |
| 5 | 84 | 0.35 | 0.75 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 3225 Ų buried · 55 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 modified (engineered).
Compared structures
- 3GE5 · Crystal structure of a putative nad(p)h:fmn oxidoreductase (pg0310) from porphyromonas… · 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
- Every structure of UniProt Q7MX99
- Elsewhere: RCSB PDB 3GE5 · PDBe 3GE5 · UniProt Q7MX99
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