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Cryo-EM structure of parathyroid hormone receptor type 2 in complex with a tuberoinfundibular peptide of 39 residues and G protein

Analyse Cryo-EM structure of parathyroid hormone receptor type 2 in complex with a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7F16
Type: protein
Length: 1,163 residues
Chains: 6
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Parathyroid hormone 2 receptor; Tuberoinfundibular peptide of 39 residues; Guanine…
UniProt: P49190, Q96A98, P63092, P54311, P63212
Ligands: PLM, CLR
Pockets: 20 · best druggability 0.83

Structure

electron microscopy · 6 distinct chains · 40% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
R	Parathyroid hormone 2 receptor	protein	376	67% helix, 5% strand	P49190
P	Tuberoinfundibular peptide of 39 residues	protein	34	85% helix, 0% strand	Q96A98
A	Guanine nucleotide-binding protein G(S) subunit alpha isoforms short	protein	230	50% helix, 18% strand	P63092
B	Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	protein	338	8% helix, 45% strand	P54311
G	Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	protein	57	54% helix, 0% strand	P63212
N	Nanobody-35	protein	128	7% helix, 46% strand	—

Ligands and binding sites

PLM · Palmitic acid · ligand · 6 copies · chains R, A
CLR · Cholesterol · ligand · 4 copies · chains R

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.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	651	0.83	0.87	71	empty
2	1109	0.77	0.79	81	empty
3	770	0.76	0.80	53	empty
4	207	0.60	0.81	33	empty
5	350	0.59	0.76	32	empty

Interfaces

7 interfaces between chains.

B–G · 2207 Å² buried · 12 hydrogen bonds · protein-protein
R–P · 2138 Å² buried · 14 hydrogen bonds · protein-protein
A–B · 1556 Å² buried · 30 hydrogen bonds · protein-protein
A–N · 1081 Å² buried · 10 hydrogen bonds · protein-protein
R–A · 1043 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 disulfide (disulfide).

Compared structures

7F16 · Cryo-EM structure of parathyroid hormone receptor type 2 in complex with a… · the same entry in another collection · chain N against N, TM-score 1.00
P54311 · 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
P49190 · AlphaFold monomer V2.0 prediction for parathyroid hormone 2 receptor (P49190) · a predicted model of the same protein · chain R against A, TM-score 0.93
Q96A98 · AlphaFold monomer V2.0 prediction for tuberoinfundibular peptide of 39 residues (Q96A98) · a predicted model of the same protein · chain P against A, TM-score 0.78
P63212 · 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 0.69

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 P49190
Every structure of UniProt Q96A98
Every structure of UniProt P63092
Every structure of UniProt P54311
Every structure of UniProt P63212
Elsewhere: RCSB PDB 7F16 · PDBe 7F16 · UniProt P49190 · UniProt Q96A98 · UniProt P63092 · UniProt P54311 · UniProt P63212

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