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Crystal structure a thioredoxin reductase from gloeobacter violaceus bound to its electron donor
Analyse Crystal structure a thioredoxin reductase from gloeobacter violaceus bound to… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6XTF
- Type
- protein
- Length
- 822 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thioredoxin reductase; Ferredoxin
- UniProt
- Q7NMP6, Q7NFA3
- Ligands
- FAD, FES
- Pockets
- 5 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 25% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Thioredoxin reductase | protein | 315 | 26% helix, 26% strand | Q7NMP6 |
| C, D | Ferredoxin | protein | 96 | 20% helix, 34% strand | Q7NFA3 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, C, B, D
- FES · Fe2/s2 (inorganic) cluster · ligand · 2 copies · chains C, D
- ACT · Acetate ion · additive · 12 copies · chains A, B, D
- PEG · Di(hydroxyethyl)ether · additive · 11 copies · chains A, B, C, D
- PG4 · Tetraethylene glycol · additive · 3 copies · chains A, C, B
- PGE · Triethylene glycol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 790 | 0.80 | 0.83 | 83 | FAD, ACT |
| 2 | 1102 | 0.79 | 0.81 | 95 | PG4, ACT |
| 3 | 814 | 0.79 | 0.82 | 93 | FAD, PEG |
| 4 | 463 | 0.70 | 0.80 | 59 | empty |
| 5 | 191 | 0.49 | 0.76 | 29 | PEG |
Interfaces
3 interfaces between chains.
- A–C · 712 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 608 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 478 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 6XTF · Crystal structure a Thioredoxin Reductase from Gloeobacter violaceus bound to its… · 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 Q7NMP6
- Every structure of UniProt Q7NFA3
- Elsewhere: RCSB PDB 6XTF · PDBe 6XTF · UniProt Q7NMP6 · UniProt Q7NFA3
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