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. 2011 May 2;108(20):8275–8280. doi: 10.1073/pnas.1016951108

Table 1.

The rmsd between predicted ICLs and ECLs and their native counterparts

Loop GPCR Loop sequence Loop length, residue numbering rmsd*, Å rmsd, Å (Mem)
ECL1 bRh GYFVF 5, (101–105) 0.17
A2Ar STGFCAA 7, (67–73) 0.18
β1AR GTWLWG 6, (105–110) 0.27
β2AR KMWTF 5, (97–101) 0.12
ECL2 bRh VGWSRYIPEGMQCSCGIDYYTPHEETN 27, (173–199) 11.53 3.44
A2Ar GWNNCGQ(PKEGKNH)SQGCGEGQVACLFEDVVP 32, (142–173) 4.39
β1AR MHWWRDEDPQALKCYQDPGCCDFVTN 26, (179–204) 1.59
β2AR MHWYRATHQEAINCYAEETCCDFFTN 26, (171–196) 2.17
ECL3 bRh HQGSDFG 7, (278–284) 0.77
A2Ar CPDCSHAP 8, (259–266) 1.94 1.11
β1AR NRDLVP 6, (316–321) 0.50
β2AR QDNLIR 6, (299–304) 0.23
ICL1 bRh HKKLRT 6, (65–70) 0.41
A2Ar NSNLQNV 7, (34–40) 0.35
β1AR TQRLQT 6, (69–74) 0.78
β2AR FERLQT 6, (61–66) 0.27
ICL2 bRh CKPMSNFRFG 10, (140–149) 5.79 2.86
A2Ar RIPLRYNGLVT 11, (107–117) 4.15 2.63
β1AR ITSPFRYQSLMT 12, (143–154) 0.33
β2AR SPFKYQSLLT 10. (137–146) 0.46
ICL3 bRh GQLVFTVKEAAAQQQESA 18, (224–241) 8.51 8.80
A2Ar Insertion of T4 lysozyme
β1AR Insertion of T4 lysozyme
β2AR Insertion of T4 lysozyme

The sequence of the six ICL and ECL loops of bovine rhodopsin, the human A2A adenosine receptor, turkey β1 adrenergic receptor, and human β2 adrenergic receptor are listed here, except for ICL3 of A2Ar, β1AR, and β2AR, which, for crystallization purposes, is partially replaced by a T4 lysozyme.

*The rmsds are all of structures procured with methods already existing in PLOP and a set of parameters optimized for GPCRs.

Mem refers to the rmsd of the loop using the membrane method developed for this project.

ECL2 of A2Ar is missing seven crystallographic residues. The rmsd is calculated using the residues specified by the crystal structure; the missing residues are omitted in the calculation.

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