Research workbench

Native human tsh bound to human thyrotropin receptor in complex with MINIGS399 (composite structure)

Analyse Native human tsh bound to human thyrotropin receptor in complex with MINIGS399… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7T9I
Type: protein
Length: 1,532 residues
Chains: 7
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Glycoprotein hormones alpha chain; Thyrotropin subunit beta; Nanobody 35; Thyrotropin…
UniProt: P01215, P01222, A0A0A0MTJ0, P63092, P62873, P59768
Ligands: NAG
Pockets: 16 · best druggability 0.84

Structure

electron microscopy · 7 distinct chains · 28% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Glycoprotein hormones alpha chain	protein	86	5% helix, 50% strand	P01215
B	Thyrotropin subunit beta	protein	109	4% helix, 47% strand	P01222
N	Nanobody 35	protein	126	7% helix, 42% strand	—
R	Thyrotropin receptor	protein	596	42% helix, 14% strand	A0A0A0MTJ0
X	Guanine nucleotide-binding protein G(S) subunit alpha isoforms short	protein	221	47% helix, 18% strand	P63092
Y	Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	protein	338	7% helix, 46% strand	P62873
Z	Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	protein	56	66% helix, 0% strand	P59768

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, B, R

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

16 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1144	0.84	0.85	84	empty
2	510	0.83	0.89	52	empty
3	876	0.79	0.82	91	empty
4	1031	0.75	0.78	84	empty
5	821	0.75	0.80	62	empty

Interfaces

9 interfaces between chains.

A–B · 2148 Å² buried · 43 hydrogen bonds · protein-protein
Y–Z · 2081 Å² buried · 12 hydrogen bonds · protein-protein
X–Y · 1433 Å² buried · 21 hydrogen bonds · protein-protein
B–R · 1105 Å² buried · 5 hydrogen bonds · protein-protein
A–R · 1018 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 16 disulfide, 7 glycan (disulfide, N-glycosylation).

Compared structures

7T9I · Native human TSH bound to human Thyrotropin receptor in complex with miniGs399 (composite… · the same entry in another collection · chain Z against Z, 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 Y 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 A against A, TM-score 0.93
P01222 · AlphaFold monomer V2.0 prediction for thyrotropin subunit beta (P01222) · a predicted model of the same protein · chain B against A, TM-score 0.91
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 Z against A, TM-score 0.90

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 P01215
Every structure of UniProt P01222
Every structure of UniProt A0A0A0MTJ0
Every structure of UniProt P63092
Every structure of UniProt P62873
Every structure of UniProt P59768
Elsewhere: RCSB PDB 7T9I · PDBe 7T9I · UniProt P01215 · UniProt P01222 · UniProt A0A0A0MTJ0 · UniProt P63092 · UniProt P62873 · UniProt P59768

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