Research workbench
Crystal structure of the binary complex between ferredoxin: thioredoxin reductase and thioredoxin M
Analyse Crystal structure of the binary complex between ferredoxin: thioredoxin… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2PUK
- Type
- protein
- Length
- 574 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ferredoxin-thioredoxin reductase, catalytic chain; Ferredoxin-thioredoxin reductase…
- UniProt
- Q55389, Q55781, P07591
- Ligands
- SF4
- Pockets
- 6 · best druggability 0.76
Structure
x-ray diffraction · 5 distinct chains · 39% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ferredoxin-thioredoxin reductase, catalytic chain | protein | 108 | 52% helix, 6% strand | Q55389 |
| B, F | Ferredoxin-thioredoxin reductase, variable chain | protein | 73 | 12% helix, 41% strand | Q55781 |
| C | Thioredoxin M-type, chloroplast (trx-M) | protein | 106 | 35% helix, 26% strand | P07591 |
| E | Ferredoxin-thioredoxin reductase, catalytic chain | protein | 109 | 51% helix, 6% strand | Q55389 |
| G | Thioredoxin M-type, chloroplast (trx-M) | protein | 105 | 33% helix, 27% strand | P07591 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 2 copies · chains A, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1116 | 0.76 | 0.78 | 71 | empty |
| 2 | 202 | 0.54 | 0.78 | 44 | SF4 |
| 3 | 71 | 0.49 | 0.84 | 19 | empty |
| 4 | 60 | 0.44 | 0.83 | 17 | empty |
| 5 | 75 | 0.36 | 0.76 | 11 | empty |
Interfaces
8 interfaces between chains.
- E–F · 916 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 890 Ų buried · 13 hydrogen bonds · protein-protein
- E–G · 815 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 798 Ų buried · 6 hydrogen bonds · protein-protein
- A–E · 157 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 2PUK · Crystal structure of the binary complex between ferredoxin: thioredoxin reductase and… · the same entry in another collection · chain G against G, TM-score 1.00
- 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 0.98
- P07591 · AlphaFold monomer V2.0 prediction for thioredoxin M-type, chloroplastic (P07591) · a predicted model of the same protein · chain G against A, TM-score 0.98
- 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 0.94
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 P07591
- Elsewhere: RCSB PDB 2PUK · PDBe 2PUK · UniProt Q55389 · UniProt Q55781 · UniProt P07591
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