MolNFT v1 · #157537 · protein
2-OXOGLUTARATE:FERREDOXIN oxidoreductase from magnetococcus marinus with 2-oxoglutarate, coenzyme a and succinyl-CoA bound
6N2O · Pyruvate FLAVODOXIN/FERREDOXIN oxidoreductase domain protein: “2-OXOGLUTARATE:FERREDOXIN oxidoreductase from magnetococcus marinus with 2-oxoglutarate, coenzyme a and…”. X-ray diffraction, 6 ligands (SF4, TPP, AKG), 15 pockets (best…
- PDB
- 6N2O
- 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, AKG, COA, SCA, MG
- Pockets
- 15 · best druggability 0.82
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, 21% strand | A0L8G4 |
| B, D | Pyruvate FERREDOXIN/FLAVODOXIN oxidoreductase, beta subunit | protein | 291 | 37% helix, 19% 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
- AKG · 2-oxoglutaric acid · ligand · chains A, B, C
- COA · Coenzyme A · ligand · chains A, B
- SCA · Succinyl-coenzyme A · ligand · chains A, C, D
- MG · Magnesium ion · metal · 2 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1101 | 0.82 | 0.83 | 101 | SCA, TPP, MG |
| 2 | 1181 | 0.81 | 0.82 | 130 | AKG, SF4, TPP, MG |
| 3 | 342 | 0.60 | 0.77 | 48 | empty |
| 4 | 333 | 0.59 | 0.77 | 46 | empty |
| 5 | 287 | 0.56 | 0.76 | 42 | empty |
Interfaces
6 interfaces between chains.
- A–C · 2574 Ų buried · 47 hydrogen bonds · protein-protein
- A–D · 2335 Ų buried · 32 hydrogen bonds · protein-protein
- B–C · 2325 Ų buried · 30 hydrogen bonds · protein-protein
- B–D · 1307 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 1054 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 6N2O · 2-oxoglutarate:ferredoxin oxidoreductase from Magnetococcus marinus with 2-oxoglutarate… · 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 6N2O · PDBe 6N2O · UniProt A0L8G4 · UniProt A0L8G5
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