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The crystal structure of the mutant R82E of thioredoxin from alicyclobacillus acidocaldarius
Analyse The crystal structure of the mutant R82E of thioredoxin from alicyclobacillus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1NW2
- Type
- protein
- Length
- 840 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thioredoxin
- EC
- 1.8.1.9
- UniProt
- P80579
- Ligands
- ZN
- Pockets
- 9 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 32% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | Thioredoxin (EC 1.8.1.9) | protein | 105 | 32% helix, 28% strand | P80579 |
Ligands and binding sites
- ZN · Zinc ion · metal · 9 copies · chains A, B, H, C, D, E, F, G
- ACT · Acetate ion · additive · 9 copies · chains A, B, H, C, E, D, F, G
- CAC · Cacodylate ion · additive · 2 copies · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 692 | 0.82 | 0.85 | 91 | empty |
| 2 | 501 | 0.79 | 0.86 | 63 | empty |
| 3 | 130 | 0.49 | 0.79 | 21 | empty |
| 4 | 109 | 0.46 | 0.79 | 19 | empty |
| 5 | 127 | 0.46 | 0.78 | 21 | empty |
Interfaces
13 interfaces between chains.
- A–D · 577 Ų buried · 5 hydrogen bonds · protein-protein
- E–H · 558 Ų buried · 3 hydrogen bonds · protein-protein
- G–H · 548 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 541 Ų buried · 3 hydrogen bonds · protein-protein
- F–G · 537 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 1NW2 · The crystal structure of the mutant R82E of Thioredoxin from Alicyclobacillus… · the same entry in another collection · chain H against H, TM-score 1.00
- P80579 · AlphaFold monomer V2.0 prediction for thioredoxin (P80579) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P80579
- Elsewhere: RCSB PDB 1NW2 · PDBe 1NW2 · UniProt P80579
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