Research workbench
Crystal structure of mus musculus iodotyrosine deiodinase (iyd) bound to FMN and mono-iodotyrosine (mit)
Analyse Crystal structure of mus musculus iodotyrosine deiodinase (iyd) bound to FMN… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3GFD
- Type
- protein
- Length
- 439 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Iodotyrosine dehalogenase 1
- UniProt
- Q9DCX8
- Ligands
- FMN, IYR
- Pockets
- 6 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Iodotyrosine dehalogenase 1 | protein | 220 | 43% helix, 19% strand | Q9DCX8 |
| B | Iodotyrosine dehalogenase 1 | protein | 219 | 44% helix, 20% strand | Q9DCX8 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · 2 copies · chains A, B
- IYR · 3-iodo-tyrosine · ligand · 2 copies · chains A, B
- GOL · Glycerol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 335 | 0.80 | 0.90 | 49 | FMN, IYR |
| 2 | 378 | 0.80 | 0.89 | 55 | FMN, IYR |
| 3 | 69 | 0.37 | 0.78 | 18 | empty |
| 4 | 62 | 0.32 | 0.76 | 18 | empty |
| 5 | 65 | 0.32 | 0.75 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 5343 Ų buried · 70 hydrogen bonds · protein-protein
Compared structures
- 3GFD · Crystal structure of Mus musculus iodotyrosine deiodinase (IYD) bound to FMN and… · the same entry in another collection · chain B against B, TM-score 1.00
- Q9DCX8 · AlphaFold monomer V2.0 prediction for iodotyrosine deiodinase 1 (Q9DCX8) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 3GFD · PDBe 3GFD · UniProt Q9DCX8
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.