Research workbench
Crystal structure of the tsh receptor in complex with a thyroid- stimulating autoantibody
Analyse Crystal structure of the tsh receptor in complex with a thyroid- stimulating… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3G04
- Type
- protein
- Length
- 655 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Human thyroid stimulating autoantibody M22 light chain; Human thyroid stimulating…
- UniProt
- P16473
- Ligands
- NAG, ZN
- Pockets
- 8 · best druggability 0.58
Structure
x-ray diffraction · 3 distinct chains · 5% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Human thyroid stimulating autoantibody M22 light chain | protein | 212 | 7% helix, 50% strand | — |
| B | Human thyroid stimulating autoantibody M22 heavy chain | protein | 215 | 8% helix, 53% strand | — |
| C | Thyrotropin receptor | protein | 228 | 0% helix, 33% strand | P16473 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, C
- ZN · Zinc ion · metal · 5 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 53 | 0.58 | 0.91 | 18 | ZN |
| 2 | 110 | 0.58 | 0.86 | 30 | empty |
| 3 | 227 | 0.56 | 0.78 | 31 | empty |
| 4 | 221 | 0.48 | 0.75 | 34 | empty |
| 5 | 82 | 0.47 | 0.81 | 19 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1747 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 780 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 623 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 glycan, 5 disulfide (N-glycosylation, disulfide).
Compared structures
- 3G04 · Crystal structure of the TSH receptor in complex with a thyroid-stimulating autoantibody · the same entry in another collection · chain A against A, TM-score 1.00
- P16473 · AlphaFold monomer V2.0 prediction for thyrotropin receptor (P16473) · a predicted model of the same protein · chain C 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 P16473
- Elsewhere: RCSB PDB 3G04 · PDBe 3G04 · UniProt P16473
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