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The crystal structure of human iyd THR239 mutant with ligand 3- fluorotyrosine (F-tyr)
Analyse The crystal structure of human iyd THR239 mutant with ligand 3- fluorotyrosine… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5YAK
- Type
- protein
- Length
- 1,303 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Iodotyrosine deiodinase 1
- EC
- 1.21.1.1
- UniProt
- Q6PHW0
- Ligands
- FMN, YOF
- Pockets
- 18 · best druggability 0.83
Structure
x-ray diffraction · 5 distinct chains · 43% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Iodotyrosine deiodinase 1 (EC 1.21.1.1) | protein | 215 | 44% helix, 19% strand | Q6PHW0 |
| B | Iodotyrosine deiodinase 1 (EC 1.21.1.1) | protein | 218 | 43% helix, 20% strand | Q6PHW0 |
| C | Iodotyrosine deiodinase 1 (EC 1.21.1.1) | protein | 217 | 44% helix, 21% strand | Q6PHW0 |
| D | Iodotyrosine deiodinase 1 (EC 1.21.1.1) | protein | 215 | 42% helix, 18% strand | Q6PHW0 |
| E, F | Iodotyrosine deiodinase 1 (EC 1.21.1.1) | protein | 219 | 43% helix, 21% strand | Q6PHW0 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · 6 copies · chains A, F, B, C, D, E
- YOF · 3-fluorotyrosine · ligand · 6 copies · chains A, F, B, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 328 | 0.83 | 0.93 | 46 | FMN, YOF |
| 2 | 435 | 0.82 | 0.89 | 59 | FMN, YOF |
| 3 | 413 | 0.82 | 0.90 | 58 | FMN, YOF |
| 4 | 405 | 0.81 | 0.89 | 60 | FMN, YOF |
| 5 | 413 | 0.81 | 0.89 | 55 | FMN, YOF |
Interfaces
9 interfaces between chains.
- B–C · 5060 Ų buried · 58 hydrogen bonds · protein-protein
- D–E · 5059 Ų buried · 52 hydrogen bonds · protein-protein
- A–F · 4801 Ų buried · 51 hydrogen bonds · protein-protein
- C–E · 266 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 182 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5YAK · The crystal structure of human IYD Thr239 mutant with ligand 3-Fluorotyrosine (F-Tyr) · the same entry in another collection · chain F against F, TM-score 1.00
- Q6PHW0 · AlphaFold monomer V2.0 prediction for iodotyrosine deiodinase 1 (Q6PHW0) · a predicted model of the same protein · chain E 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 Q6PHW0
- Elsewhere: RCSB PDB 5YAK · PDBe 5YAK · UniProt Q6PHW0
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