Research workbench
Crystal structure of thyroxine-binding globulin complexed with thyroxine-fluoresein
Analyse Crystal structure of thyroxine-binding globulin complexed with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2XN6
- Type
- protein
- Length
- 371 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thyroxine-binding globulin
- UniProt
- P05543
- Ligands
- F6Y, T44, CA
- Pockets
- 3 · best druggability 0.59
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thyroxine-binding globulin | protein | 337 | 34% helix, 38% strand | P05543 |
| B | Thyroxine-binding globulin | protein | 34 | 0% helix, 56% strand | P05543 |
Ligands and binding sites
- F6Y · 3',6'-dihydroxy-3-oxo-3H-spiro[2-benzofuran-1,9'-xanthene]-6-carboxylic acid · ligand · chains A, B
- T44 · 3,5,3',5'-tetraiodo-L-thyronine · ligand · chains A, B
- CA · Calcium ion · metal · 7 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 7 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 195 | 0.59 | 0.81 | 20 | T44 |
| 2 | 118 | 0.45 | 0.78 | 20 | EDO |
| 3 | 53 | 0.27 | 0.74 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 2478 Ų buried · 37 hydrogen bonds · protein-protein
Compared structures
- 2XN6 · Crystal structure of thyroxine-binding globulin complexed with thyroxine-fluoresein · the same entry in another collection · chain A against A, TM-score 1.00
- P05543 · AlphaFold monomer V2.0 prediction for thyroxine-binding globulin (P05543) · a predicted model of the same protein · chain A against A, TM-score 0.92
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 P05543
- Elsewhere: RCSB PDB 2XN6 · PDBe 2XN6 · UniProt P05543
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