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Crystal structure of iodotyrosine deiodinase (iyd) in the semiquinone form bound to FMN and 3-iodo-L-tyrosine
Analyse Crystal structure of iodotyrosine deiodinase (iyd) in the semiquinone form… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6TYK
- Type
- protein
- Length
- 369 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Iodotyrosine deiodinase
- EC
- 1.21.1.1
- UniProt
- B9K712
- Ligands
- IYR, FMN, CL
- Pockets
- 3 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Iodotyrosine deiodinase (EC 1.21.1.1) | protein | 185 | 44% helix, 17% strand | B9K712 |
| B | Iodotyrosine deiodinase (EC 1.21.1.1) | protein | 184 | 44% helix, 17% strand | B9K712 |
Ligands and binding sites
- IYR · 3-iodo-tyrosine · ligand · 3 copies · chains A, B
- FMN · Flavin mononucleotide · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 437 | 0.79 | 0.87 | 48 | FMN, IYR |
| 2 | 428 | 0.78 | 0.86 | 46 | FMN, IYR, CL |
| 3 | 54 | 0.26 | 0.73 | 9 | empty |
Interfaces
1 interface between chains.
- A–B · 3233 Ų buried · 45 hydrogen bonds · protein-protein
Compared structures
- 6TYK · Crystal structure of iodotyrosine deiodinase (IYD) in the semiqui form bound to FMN and… · the same entry in another collection · chain A against A, TM-score 1.00
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 B9K712
- Elsewhere: RCSB PDB 6TYK · PDBe 6TYK · UniProt B9K712
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