MolNFT v1 · #105547 · protein
Streptomyces globisporus C-1027 NADH:FAD oxidoreductase SGCE6 in complex with NAD and FAD fragments
4R82: “Streptomyces globisporus C-1027 NADH:FAD oxidoreductase SGCE6 in complex with NAD and FAD fragments”. X-ray diffraction, 5 ligands (NAD, FAD, CA), 2 pockets (best druggability 0.62). MolNFT v1 #105547 on GenesisL1: 3D structure…
- PDB
- 4R82
- Type
- protein
- Length
- 331 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Oxidoreductase
- UniProt
- Q8GME2
- Ligands
- NAD, FAD, CA, MG, CL
- Pockets
- 2 · best druggability 0.62
Structure
x-ray diffraction · 2 distinct chains · 13% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Oxidoreductase | protein | 166 | 13% helix, 43% strand | Q8GME2 |
| B | Oxidoreductase | protein | 165 | 13% helix, 44% strand | Q8GME2 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
- CA · Calcium ion · metal · 3 copies · chains A, B
- MG · Magnesium ion · metal · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
- ACT · Acetate ion · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 385 | 0.62 | 0.77 | 49 | MG, NAD, FAD |
| 2 | 391 | 0.60 | 0.76 | 41 | NAD, FAD |
Interfaces
1 interface between chains.
- A–B · 2979 Ų buried · 44 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified (engineered).
Compared structures
- 4R82 · Streptomyces globisporus C-1027 NADH:FAD oxidoreductase SgcE6 in complex with NAD and FAD… · 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 Q8GME2
- Elsewhere: RCSB PDB 4R82 · PDBe 4R82 · UniProt Q8GME2
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