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Cryo-EM structure of N-terminal modified human vasoactive intestinal polypeptide receptor 2 (VIP2R) in complex with PACAP27 and Gs

Analyse Cryo-EM structure of N-terminal modified human vasoactive intestinal… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7WBJ
Type: protein
Length: 1,146 residues
Chains: 6
Method: electron microscopy
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 3.42
Source: Bos taurus; Homo sapiens; Rattus norvegicus; synthetic construct; SYNTHETIC…
Molecule: Vasoactive intestinal polypeptide receptor 2; Pituitary adenylate cyclase-activating…
UniProt: P41587, P18509, P04896, P54311, P63212
Pockets: 15 · best druggability 0.80

Structure

electron microscopy · resolution 3.42 · 6 distinct chains · 35% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
R	Vasoactive intestinal polypeptide receptor 2	protein	359	59% helix, 4% strand	P41587
L	Pituitary adenylate cyclase-activating polypeptide 27	protein	27	93% helix, 0% strand	P18509
A	Guanine nucleotide-binding protein G(s) subunit alpha isoforms short	protein	237	45% helix, 16% strand	P04896
B	Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	protein	340	7% helix, 34% strand	P54311
G	Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	protein	55	49% helix, 0% strand	P63212
N	Nanobody-35	protein	128	0% helix, 38% strand	—

Pockets

15 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	683	0.80	0.85	52	empty
2	804	0.73	0.78	58	empty
3	1172	0.71	0.75	87	empty
4	349	0.69	0.82	48	empty
5	165	0.65	0.86	26	empty

Interfaces

7 interfaces between chains.

B–G · 2021 Å² buried · 12 hydrogen bonds · protein-protein
R–L · 1526 Å² buried · 8 hydrogen bonds · protein-protein
A–B · 1420 Å² buried · 14 hydrogen bonds · protein-protein
R–A · 985 Å² buried · 12 hydrogen bonds · protein-protein
A–N · 935 Å² buried · 8 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 disulfide (disulfide).

Compared structures

7WBJ · Cryo-EM structure of N-terminal modified human vasoactive intestinal polypeptide receptor… · the same entry in another collection · chain R against R, 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 0.98
P41587 · AlphaFold monomer V2.0 prediction for vasoactive intestinal polypeptide receptor 2… · a predicted model of the same protein · chain R against A, TM-score 0.89
P04896 · 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 0.83
P18509 · AlphaFold monomer V2.0 prediction for pituitary adenylate cyclase- activating polypeptide… · a predicted model of the same protein · chain L against A, TM-score 0.79
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 0.60

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 P41587
Every structure of UniProt P18509
Every structure of UniProt P04896
Every structure of UniProt P54311
Every structure of UniProt P63212
Elsewhere: RCSB PDB 7WBJ · PDBe 7WBJ · UniProt P41587 · UniProt P18509 · UniProt P04896 · UniProt P54311 · UniProt P63212

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