Research workbench
Tshr-thyroid stimulating hormone-gs-ML109 complex
Analyse Tshr-thyroid stimulating hormone-gs-ML109 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7XW5
- Type
- protein
- Length
- 1,522 residues
- Chains
- 7
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Guanine nucleotide-binding protein G(S) subunit alpha isoforms short; Guanine…
- UniProt
- P63094, P62873, P59768, P16473, P01215, P01222
- Ligands
- CLR, PLM, HOI, NAG
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 7 distinct chains · 28% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Guanine nucleotide-binding protein G(S) subunit alpha isoforms short | protein | 235 | 49% helix, 17% strand | P63094 |
| B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | protein | 338 | 8% helix, 47% strand | P62873 |
| G | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | protein | 57 | 60% helix, 0% strand | P59768 |
| N | NANOBODY35 | protein | 128 | 5% helix, 46% strand | — |
| R | Thyrotropin receptor | protein | 572 | 42% helix, 13% strand | P16473 |
| X | Glycoprotein hormones alpha chain | protein | 87 | 5% helix, 51% strand | P01215 |
| Y | Thyrotropin subunit beta | protein | 105 | 0% helix, 50% strand | P01222 |
Ligands and binding sites
- CLR · Cholesterol · ligand · 14 copies · chains R
- PLM · Palmitic acid · ligand · 5 copies · chains R
- HOI · ~{N}-[4-[[2-methoxy-5-[(2~{S})-5-oxidanyl-4-oxidanylidene-3-(phenylmethyl)-1,2-dihydroquinazolin-2-yl]phenyl]methoxy]phenyl]ethanamide · ligand · chains R
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 7 copies · chains R, X, Y
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 533 | 0.84 | 0.90 | 54 | HOI |
| 2 | 930 | 0.84 | 0.86 | 79 | empty |
| 3 | 691 | 0.74 | 0.80 | 51 | empty |
| 4 | 1111 | 0.72 | 0.76 | 86 | empty |
| 5 | 433 | 0.71 | 0.82 | 55 | empty |
Interfaces
9 interfaces between chains.
- X–Y · 2436 Ų buried · 32 hydrogen bonds · protein-protein
- B–G · 2272 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 1482 Ų buried · 21 hydrogen bonds · protein-protein
- A–R · 1041 Ų buried · 5 hydrogen bonds · protein-protein
- R–X · 961 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 17 disulfide, 7 glycan (disulfide, N-glycosylation).
Compared structures
- 7XW5 · TSHR-thyroid stimulating hormone-Gs-ML109 complex · the same entry in another collection · chain Y against Y, TM-score 1.00
- P62873 · AlphaFold monomer V2.0 prediction for guanine nucleotide-binding protein G(I)/G(S)/G(T)… · a predicted model of the same protein · chain B against A, TM-score 0.99
- P01215 · AlphaFold monomer V2.0 prediction for glycoprotein hormones alpha chain (P01215) · a predicted model of the same protein · chain X against A, TM-score 0.92
- P59768 · AlphaFold monomer V2.0 prediction for guanine nucleotide-binding protein G(I)/G(S)/G(O)… · a predicted model of the same protein · chain G against A, TM-score 0.90
- P63094 · AlphaFold monomer V2.0 prediction for guanine nucleotide-binding protein G(S) subunit… · a predicted model of the same protein · chain A against A, TM-score 0.89
- P01222 · AlphaFold monomer V2.0 prediction for thyrotropin subunit beta (P01222) · a predicted model of the same protein · chain Y against A, TM-score 0.89
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 P63094
- Every structure of UniProt P62873
- Every structure of UniProt P59768
- Every structure of UniProt P16473
- Every structure of UniProt P01215
- Every structure of UniProt P01222
- Elsewhere: RCSB PDB 7XW5 · PDBe 7XW5 · UniProt P63094 · UniProt P62873 · UniProt P59768 · UniProt P16473 · UniProt P01215 · UniProt P01222
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