MolNFT v1 · #157536 · protein
Crystal structure of 2-OXOGLUTARATE:FERREDOXIN oxidoreductase from magnetococcus marinus
6N2N · Pyruvate FLAVODOXIN/FERREDOXIN oxidoreductase domain protein: “Crystal structure of 2-OXOGLUTARATE:FERREDOXIN oxidoreductase from magnetococcus marinus”. X-ray diffraction, 4 ligands (SF4, TPP, MG), 13 pockets (best druggability…
- PDB
- 6N2N
- Type
- protein
- Length
- 1,726 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyruvate FLAVODOXIN/FERREDOXIN oxidoreductase domain protein; Pyruvate…
- UniProt
- A0L8G4, A0L8G5
- Ligands
- SF4, TPP, MG, SO4
- Pockets
- 13 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Pyruvate FLAVODOXIN/FERREDOXIN oxidoreductase domain protein | protein | 572 | 40% helix, 22% strand | A0L8G4 |
| B, D | Pyruvate FERREDOXIN/FLAVODOXIN oxidoreductase, beta subunit | protein | 291 | 36% helix, 18% strand | A0L8G5 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 2 copies · chains A, B, C, D
- TPP · Thiamine diphosphate · ligand · 2 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 2 copies · chains B, D
- SO4 · Sulfate ion · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 968 | 0.85 | 0.86 | 127 | SO4, SF4, TPP, MG |
| 2 | 1114 | 0.83 | 0.84 | 137 | SO4, SF4, TPP |
| 3 | 311 | 0.60 | 0.78 | 51 | empty |
| 4 | 292 | 0.58 | 0.77 | 41 | empty |
| 5 | 106 | 0.45 | 0.78 | 20 | empty |
Interfaces
6 interfaces between chains.
- A–C · 2483 Ų buried · 40 hydrogen bonds · protein-protein
- B–C · 2261 Ų buried · 29 hydrogen bonds · protein-protein
- A–D · 2257 Ų buried · 31 hydrogen bonds · protein-protein
- B–D · 1325 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 988 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 6N2N · Crystal structure of 2-oxoglutarate:ferredoxin oxidoreductase from Magnetococcus marinus · 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 A0L8G4
- Every structure of UniProt A0L8G5
- Elsewhere: RCSB PDB 6N2N · PDBe 6N2N · UniProt A0L8G4 · UniProt A0L8G5
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