Research workbench
Crystal srtucture of the ternary complex between thioredoxin F, ferredoxin, and ferredoxin: thioredoxin reductase
Analyse Crystal srtucture of the ternary complex between thioredoxin F, ferredoxin, and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2PVO
- Type
- protein
- Length
- 391 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ferredoxin-thioredoxin reductase, catalytic chain; Ferredoxin-thioredoxin reductase…
- UniProt
- Q55389, Q55781, P09856, P27320
- Ligands
- SF4, FES, SO4
- Pockets
- 5 · best druggability 0.66
Structure
x-ray diffraction · 4 distinct chains · 29% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ferredoxin-thioredoxin reductase, catalytic chain | protein | 110 | 51% helix, 5% strand | Q55389 |
| B | Ferredoxin-thioredoxin reductase, variable chain | protein | 74 | 8% helix, 41% strand | Q55781 |
| C | Thioredoxin F-type, chloroplast | protein | 111 | 35% helix, 25% strand | P09856 |
| D | Ferredoxin-1 | protein | 96 | 13% helix, 25% strand | P27320 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · chains A
- FES · Fe2/s2 (inorganic) cluster · ligand · chains D
- SO4 · Sulfate ion · ion · 2 copies · chains A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 516 | 0.66 | 0.77 | 44 | SO4 |
| 2 | 198 | 0.59 | 0.81 | 23 | empty |
| 3 | 97 | 0.47 | 0.80 | 17 | empty |
| 4 | 113 | 0.36 | 0.73 | 16 | empty |
| 5 | 71 | 0.33 | 0.75 | 17 | SO4 |
Interfaces
4 interfaces between chains.
- A–B · 916 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 872 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 703 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 28 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 2PVO · Crystal srtucture of the ternary complex between thioredoxin f, ferredoxin, and… · the same entry in another collection · chain D against D, TM-score 1.00
- P09856 · AlphaFold monomer V2.0 prediction for thioredoxin F-type, chloroplastic (P09856) · a predicted model of the same protein · chain C against A, TM-score 0.99
- P27320 · AlphaFold monomer V2.0 prediction for ferredoxin-1 (P27320) · a predicted model of the same protein · chain D against A, TM-score 0.98
- Q55389 · AlphaFold monomer V2.0 prediction for ferredoxin-thioredoxin reductase, catalytic chain… · a predicted model of the same protein · chain A against A, TM-score 0.97
- Q55781 · AlphaFold monomer V2.0 prediction for ferredoxin-thioredoxin reductase, variable chain… · 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 Q55389
- Every structure of UniProt Q55781
- Every structure of UniProt P09856
- Every structure of UniProt P27320
- Elsewhere: RCSB PDB 2PVO · PDBe 2PVO · UniProt Q55389 · UniProt Q55781 · UniProt P09856 · UniProt P27320
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