Research workbench
Crystal structure of mus musculus iodotyrosine deiodinase (iyd) C217A, C239A bound to FMN
Analyse Crystal structure of mus musculus iodotyrosine deiodinase (iyd) C217A, C239A… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3TO0
- Type
- protein
- Length
- 369 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Iodotyrosine deiodinase 1
- EC
- 1.22.1.1
- UniProt
- Q9DCX8
- Ligands
- FMN, PO4
- Pockets
- 4 · best druggability 0.60
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Iodotyrosine deiodinase 1 (EC 1.22.1.1) | protein | 184 | 42% helix, 21% strand | Q9DCX8 |
| B | Iodotyrosine deiodinase 1 (EC 1.22.1.1) | protein | 185 | 43% helix, 21% strand | Q9DCX8 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
- ACT · Acetate ion · additive · 2 copies · chains A, 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 304 | 0.60 | 0.78 | 44 | ACT, FMN |
| 2 | 204 | 0.55 | 0.78 | 30 | FMN |
| 3 | 98 | 0.36 | 0.74 | 14 | empty |
| 4 | 56 | 0.29 | 0.75 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 4431 Ų buried · 62 hydrogen bonds · protein-protein
Compared structures
- 3TO0 · Crystal structure of Mus musculus iodotyrosine deiodinase (IYD) C217A, C239A bound to FMN · the same entry in another collection · chain A against A, TM-score 1.00
- Q9DCX8 · AlphaFold monomer V2.0 prediction for iodotyrosine deiodinase 1 (Q9DCX8) · 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 Q9DCX8
- Elsewhere: RCSB PDB 3TO0 · PDBe 3TO0 · UniProt Q9DCX8
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