Research workbench
2-Oxoacid:Ferredoxin Oxidoreductase 2 from Sulfolobus tokodai - pyruvate complex
Analyse 2-Oxoacid:Ferredoxin Oxidoreductase 2 from Sulfolobus tokodai - pyruvate complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5B47
- Type
- protein
- Length
- 902 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.2
- Source
- Sulfolobus tokodaii str. 7
- Molecule
- 2-oxoacid--ferredoxin oxidoreductase alpha subunit; 2-oxoacid--ferredoxin oxidoreductase…
- EC
- 1.2.7.-
- UniProt
- Q96XT2, Q96XT4
- Ligands
- PYR, SF4, TPP, MG
- Pockets
- 8 · best druggability 0.80
Structure
x-ray diffraction · resolution 2.2 · 2 distinct chains · 41% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 2-oxoacid--ferredoxin oxidoreductase alpha subunit (EC 1.2.7.-) | protein | 627 | 42% helix, 23% strand | Q96XT2 |
| B | 2-oxoacid--ferredoxin oxidoreductase beta subunit (EC 1.2.7.-) | protein | 275 | 38% helix, 20% strand | Q96XT4 |
Ligands and binding sites
- PYR · Pyruvic acid · ligand · chains A, B
- SF4 · Iron/sulfur cluster · ligand · chains A, B
- TPP · Thiamine diphosphate · ligand · chains A, B
- MG · Magnesium ion · metal · chains B
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 | 1031 | 0.80 | 0.81 | 112 | PYR, SF4, TPP, MG |
| 2 | 302 | 0.61 | 0.79 | 43 | empty |
| 3 | 154 | 0.46 | 0.76 | 26 | empty |
| 4 | 98 | 0.37 | 0.75 | 21 | empty |
| 5 | 52 | 0.36 | 0.79 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 851 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 5B47 · 2-OXOACID:FERREDOXIN oxidoreductase 2 from sulfolobus tokodai - pyruvate complex · the same entry in another collection · chain A against A, TM-score 1.00
- Q96XT2 · AlphaFold monomer V2.0 prediction for 2-OXOACID:FERREDOXIN oxidoreductase 2, subunit… · a predicted model of the same protein · chain A against A, TM-score 1.00
- Q96XT4 · AlphaFold monomer V2.0 prediction for 2-OXOACID:FERREDOXIN oxidoreductase 2, subunit beta… · a predicted model of the same protein · chain B against A, TM-score 0.93
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 Q96XT2
- Every structure of UniProt Q96XT4
- Elsewhere: RCSB PDB 5B47 · PDBe 5B47 · UniProt Q96XT2 · UniProt Q96XT4
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