MolNFT v2 · #213324 · protein

Cryo-EM structure of the PG-901-bound human melanocortin receptor 5 (MC5R)-Gs complex

8IOD · Guanine nucleotide-binding protein G(i) subunit…: “Cryo-EM structure of the PG-901-bound human melanocortin receptor 5 (MC5R)-Gs complex”. Electron microscopy at 2.59, 1 ligand (CA), 14 pockets (best druggability 0.80). MolNFT v2…

PDB: 8IOD
Type: protein
Length: 1,023 residues
Chains: 6
Method: electron microscopy
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 2.59
Source: Bos taurus; Homo sapiens; Influenza A virus (strain A/Victoria/3/1975 H3N2)…
Molecule: Guanine nucleotide-binding protein G(i) subunit alpha-1,Guanine nucleotide-binding…
UniProt: P63096, P63092, P62873, P63212, P03435, P33032
Ligands: CA
Pockets: 14 · best druggability 0.80

Structure

electron microscopy · resolution 2.59 · 6 distinct chains · 35% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Guanine nucleotide-binding protein G(i) subunit alpha-1,Guanine nucleotide-binding protein G(s) subunit alpha isoforms short	protein	234	42% helix, 15% strand	P63096, P63092
B	Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1,HiBiT	protein	334	6% helix, 48% strand	P62873
G	Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	protein	52	54% helix, 0% strand	P63212
L	Pg-901	protein	7	0% helix, 0% strand	—
N	Nanobody-35	protein	126	7% helix, 44% strand	—
R	HA signal peptide,Melanocortin receptor 5,LgBiT subunit	protein	270	77% helix, 0% strand	P03435, P33032

Ligands and binding sites

CA · Calcium ion · metal · chains L, R

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

Pockets

14 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	638	0.80	0.85	55	empty
2	984	0.77	0.79	80	empty
3	369	0.70	0.82	47	empty
4	692	0.69	0.77	51	empty
5	131	0.66	0.89	26	empty

Interfaces

7 interfaces between chains.

B–G · 2142 Å² buried · 18 hydrogen bonds · protein-protein
A–B · 1561 Å² buried · 21 hydrogen bonds · protein-protein
A–R · 1404 Å² buried · 11 hydrogen bonds · protein-protein
A–N · 911 Å² buried · 15 hydrogen bonds · protein-protein
L–R · 771 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide, 2 modified (disulfide, nonstandard).

Compared structures

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 0.98
P33032 · AlphaFold monomer V2.0 prediction for melanocortin receptor 5 (P33032) · a predicted model of the same protein · chain R against A, TM-score 0.91
P63092 · 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 0.85
P63096 · AlphaFold monomer V2.0 prediction for guanine nucleotide-binding protein G(I) subunit… · a predicted model of the same protein · chain A against A, TM-score 0.74
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 0.66

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 P63096
Every structure of UniProt P63092
Every structure of UniProt P62873
Every structure of UniProt P63212
Every structure of UniProt P03435
Every structure of UniProt P33032
Elsewhere: RCSB PDB 8IOD · PDBe 8IOD · UniProt P63096 · UniProt P63092 · UniProt P62873 · UniProt P63212 · UniProt P03435 · UniProt P33032

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