Research workbench
Crystal structure of a thioredoxine reductase (trxb) from staphylococcus aureus subsp. aureus MU50 at 1.80 a resolution
Analyse Crystal structure of a thioredoxine reductase (trxb) from staphylococcus aureus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4GCM
- Type
- protein
- Length
- 617 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thioredoxin reductase
- EC
- 1.8.1.9
- UniProt
- P66011
- Ligands
- FAD, NAP, CL
- Pockets
- 4 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 28% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thioredoxin reductase (EC 1.8.1.9) | protein | 308 | 29% helix, 30% strand | P66011 |
| B | Thioredoxin reductase (EC 1.8.1.9) | protein | 309 | 28% helix, 29% strand | P66011 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · chains B
- CL · Chloride ion · ion · 2 copies · chains A, B
- GOL · Glycerol · additive · 3 copies · chains A, B
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 601 | 0.77 | 0.83 | 68 | FAD |
| 2 | 1127 | 0.77 | 0.79 | 122 | GOL, NAP |
| 3 | 583 | 0.77 | 0.83 | 61 | FAD |
| 4 | 77 | 0.32 | 0.74 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 2155 Ų buried · 34 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 modified (engineered).
Compared structures
- 4GCM · Crystal structure of a thioredoxine reductase (trxB) from Staphylococcus aureus subsp.… · the same entry in another collection · chain A against A, TM-score 1.00
- P66011 · AlphaFold monomer V2.0 prediction for thioredoxin reductase (P66011) · a predicted model of the same protein · chain B against A, TM-score 0.77
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 P66011
- Elsewhere: RCSB PDB 4GCM · PDBe 4GCM · UniProt P66011
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