MolNFT v1 · #72411 · protein

Crystal structure of the ectodomain complex of the cgrp receptor, a class-B GPCR, reveals the site of drug antagonism

3N7P · Calcitonin gene-related peptide type 1 receptor: “Crystal structure of the ectodomain complex of the cgrp receptor, a class-B GPCR, reveals the site of drug…”. X-ray diffraction, 1 ligand (SO4), 13 pockets (best druggability 0.73).…

PDB: 3N7P
Type: protein
Length: 703 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Calcitonin gene-related peptide type 1 receptor; Receptor activity-modifying protein 1
UniProt: Q16602, O60894
Ligands: SO4
Pockets: 13 · best druggability 0.73

Structure

x-ray diffraction · 7 distinct chains · 42% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Calcitonin gene-related peptide type 1 receptor	protein	100	17% helix, 24% strand	Q16602
B	Calcitonin gene-related peptide type 1 receptor	protein	99	19% helix, 24% strand	Q16602
C	Calcitonin gene-related peptide type 1 receptor	protein	68	24% helix, 16% strand	Q16602
D	Receptor activity-modifying protein 1	protein	90	69% helix, 0% strand	O60894
E, F	Receptor activity-modifying protein 1	protein	79	75% helix, 0% strand	O60894
J	Calcitonin gene-related peptide type 1 receptor	protein	97	25% helix, 25% strand	Q16602
R	Receptor activity-modifying protein 1	protein	91	68% helix, 0% strand	O60894

Ligands and binding sites

SO4 · Sulfate ion · ion · 16 copies · chains A, R, D, B, J, E

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

Pockets

13 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	168	0.73	0.91	31	SO4
2	739	0.73	0.79	62	SO4
3	63	0.71	0.97	13	SO4
4	58	0.71	0.98	15	SO4
5	177	0.63	0.84	27	empty

Interfaces

11 interfaces between chains.

B–R · 1037 Å² buried · 10 hydrogen bonds · protein-protein
A–D · 999 Å² buried · 11 hydrogen bonds · protein-protein
E–J · 800 Å² buried · 7 hydrogen bonds · protein-protein
A–R · 773 Å² buried · 8 hydrogen bonds · protein-protein
B–D · 730 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 22 disulfide, 12 modified (disulfide, engineered).

Compared structures

3N7P · Crystal structure of the ectodomain complex of the CGRP receptor, a Class-B GPCR, reveals… · the same entry in another collection · chain R against R, TM-score 1.00
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
Q16602 · AlphaFold monomer V2.0 prediction for calcitonin gene-related peptide type 1 receptor… · a predicted model of the same protein · chain J against A, TM-score 0.97

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 Q16602
Every structure of UniProt O60894
Elsewhere: RCSB PDB 3N7P · PDBe 3N7P · UniProt Q16602 · UniProt O60894

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