Research workbench
Design of disulfide-linked thioredoxin dimers and multimers through analysis of crystal contacts
Analyse Design of disulfide-linked thioredoxin dimers and multimers through analysis of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2EIR
- Type
- protein
- Length
- 428 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thioredoxin 1
- UniProt
- P0AA25
- Ligands
- CU
- Pockets
- 2 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 32% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Thioredoxin 1 | protein | 107 | 32% helix, 29% strand | P0AA25 |
Ligands and binding sites
- CU · Copper (II) ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 672 | 0.71 | 0.78 | 76 | empty |
| 2 | 186 | 0.70 | 0.87 | 28 | empty |
Interfaces
5 interfaces between chains.
- C–D · 604 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 559 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 156 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 123 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 41 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 2EIR · Design of Disulfide-linked Thioredoxin Dimers and Multimers Through Analysis of Crystal… · the same entry in another collection · chain A against A, TM-score 1.00
- P0AA25 · AlphaFold monomer V2.0 prediction for thioredoxin 1 (P0AA25) · 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 P0AA25
- Elsewhere: RCSB PDB 2EIR · PDBe 2EIR · UniProt P0AA25
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