MolNFT v1 · #122984 · protein
Structure of a thioredoxin reductase from gloeobacter violaceus
5J60: “Structure of a thioredoxin reductase from gloeobacter violaceus”. X-ray diffraction, 2 ligands (FAD, CA), 11 pockets (best druggability 0.80). MolNFT v1 #122984 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5J60
- Type
- protein
- Length
- 1,225 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thioredoxin reductase
- UniProt
- Q7NMP6
- Ligands
- FAD, CA
- Pockets
- 11 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 27% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thioredoxin reductase | protein | 316 | 27% helix, 27% strand | Q7NMP6 |
| B | Thioredoxin reductase | protein | 316 | 27% helix, 27% strand | Q7NMP6 |
| C | Thioredoxin reductase | protein | 296 | 27% helix, 23% strand | Q7NMP6 |
| D | Thioredoxin reductase | protein | 297 | 27% helix, 24% strand | Q7NMP6 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 4 copies · chains A, D, B, C
- CA · Calcium ion · metal · 2 copies · chains A, D, B
- PG4 · Tetraethylene glycol · additive · 2 copies · chains A, D, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 617 | 0.80 | 0.85 | 76 | FAD |
| 2 | 575 | 0.80 | 0.86 | 73 | FAD |
| 3 | 501 | 0.78 | 0.85 | 68 | FAD |
| 4 | 466 | 0.76 | 0.85 | 70 | FAD |
| 5 | 679 | 0.68 | 0.76 | 54 | empty |
Interfaces
3 interfaces between chains.
- A–D · 1670 Ų buried · 22 hydrogen bonds · protein-protein
- A–C · 449 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 445 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 5J60 · Structure of a thioredoxin reductase from Gloeobacter violaceus · 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
- Elsewhere: RCSB PDB 5J60 · PDBe 5J60 · UniProt Q7NMP6
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