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Cryo-EM structure of the neuromedin U-bound neuromedin U receptor 2-gq protein complex

Analyse Cryo-EM structure of the neuromedin U-bound neuromedin U receptor 2-gq protein… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7W55
Type: protein
Length: 1,166 residues
Chains: 6
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Guanine nucleotide-binding protein G(Q) subunit alpha; Guanine nucleotide-binding protein…
UniProt: P62873, P48645, P59768
Pockets: 13 · best druggability 0.82

Structure

electron microscopy · 6 distinct chains · 37% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Guanine nucleotide-binding protein G(Q) subunit alpha	protein	232	49% helix, 17% strand	—
B	Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	protein	338	8% helix, 48% strand	P62873
C	Neuromedin-U-25	protein	8	0% helix, 0% strand	P48645
E	SCFV16	protein	231	6% helix, 47% strand	—
G	Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	protein	54	69% helix, 0% strand	P59768
R	Neuromedin-U receptor 2	protein	303	80% helix, 2% strand	—

Pockets

13 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	662	0.82	0.86	58	empty
2	91	0.77	0.98	24	empty
3	1082	0.77	0.79	73	empty
4	550	0.68	0.78	59	empty
5	310	0.61	0.79	51	empty

Interfaces

7 interfaces between chains.

B–G · 2022 Å² buried · 14 hydrogen bonds · protein-protein
A–R · 1496 Å² buried · 18 hydrogen bonds · protein-protein
A–B · 1490 Å² buried · 28 hydrogen bonds · protein-protein
C–R · 947 Å² buried · 22 hydrogen bonds · protein-protein
A–E · 619 Å² buried · 11 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 disulfide (disulfide).

Compared structures

7W55 · Cryo-EM structure of the neuromedin U-bound neuromedin U receptor 2-Gq protein complex · the same entry in another collection · chain R against R, 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
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 0.96
P48645 · AlphaFold monomer V2.0 prediction for neuromedin-U (P48645) · a predicted model of the same protein · chain C against A, TM-score 0.56

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 P62873
Every structure of UniProt P48645
Every structure of UniProt P59768
Elsewhere: RCSB PDB 7W55 · PDBe 7W55 · UniProt P62873 · UniProt P48645 · UniProt P59768

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