Research workbench

Cryo-EM structure of the active, gs-protein complexed, human cgrp receptor

Analyse Cryo-EM structure of the active, gs-protein complexed, human cgrp receptor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6E3Y
Type: protein
Length: 1,194 residues
Chains: 7
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Calcitonin gene-related peptide 1; Nanobody 35; Guanine nucleotide-binding protein G(S)…
UniProt: P06881, P63092, P62873, P59768, Q16602, O60894
Ligands: NH2
Pockets: 16 · best druggability 0.81

Structure

electron microscopy · 7 distinct chains · 39% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
P	Calcitonin gene-related peptide 1	protein	34	35% helix, 0% strand	P06881
N	Nanobody 35	protein	126	7% helix, 44% strand	—
A	Guanine nucleotide-binding protein G(S) subunit alpha isoforms short	protein	188	45% helix, 18% strand	P63092
B	Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	protein	336	7% helix, 45% strand	P62873
G	Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	protein	49	53% helix, 0% strand	P59768
R	Calcitonin gene-related peptide type 1 receptor	protein	346	65% helix, 7% strand	Q16602
E	Receptor activity-modifying protein 1	protein	115	74% helix, 0% strand	O60894

Ligands and binding sites

NH2 · Amino group · ion · chains P, 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, 11 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	614	0.81	0.86	55	empty
2	1048	0.76	0.79	69	empty
3	140	0.70	0.91	25	empty
4	498	0.68	0.79	36	empty
5	595	0.67	0.77	51	empty

Interfaces

9 interfaces between chains.

R–E · 2152 Å² buried · 11 hydrogen bonds · protein-protein
P–R · 2092 Å² buried · 22 hydrogen bonds · protein-protein
B–G · 2068 Å² buried · 13 hydrogen bonds · protein-protein
A–B · 1572 Å² buried · 23 hydrogen bonds · protein-protein
A–R · 1125 Å² buried · 9 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 9 disulfide (disulfide).

Compared structures

6E3Y · Cryo-EM structure of the active, Gs-protein complexed, human CGRP receptor · the same entry in another collection · chain E against E, 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
O60894 · AlphaFold monomer V2.0 prediction for receptor activity-modifying protein 1 (O60894) · a predicted model of the same protein · chain E against A, TM-score 0.98
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 0.92
P06881 · AlphaFold monomer V2.0 prediction for calcitonin gene-related peptide 1 (P06881) · a predicted model of the same protein · chain P against A, TM-score 0.91
Q16602 · AlphaFold monomer V2.0 prediction for calcitonin gene-related peptide type 1 receptor… · a predicted model of the same protein · chain R against A, TM-score 0.85

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 P06881
Every structure of UniProt P63092
Every structure of UniProt P62873
Every structure of UniProt P59768
Every structure of UniProt Q16602
Every structure of UniProt O60894
Elsewhere: RCSB PDB 6E3Y · PDBe 6E3Y · UniProt P06881 · UniProt P63092 · UniProt P62873 · UniProt P59768 · UniProt Q16602 · UniProt O60894

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