SARS-CoV-2 Ligands Database

HR1

HR1 (Heptad Repeat 1) is one of two heptad repeat motifs in the S2 subunit of the coronavirus spike (S) protein, the other being HR2 (Heptad Repeat 2). These regions consist of amino acid sequences repeating every seven residues, which promotes the formation of alpha-helices and coiled-coil structures.

The function of HR1 is to participate in the fusion process between the viral and cellular membranes. After activation of the S protein, HR1 interacts with HR2 to form a six-helix bundle (six-stranded coiled-coil) complex that stabilizes the post-fusion conformation of the protein. This structure brings the viral and cellular membranes close together, facilitating their fusion and allowing the viral genome to enter the host cell.

№	Extended PDB ID	PDB ID	Method	Resolution	Chain	Start	End	Macromolecules	Ligand 1	Ligand 2
1	pdb_00007ek6	7EK6	X-ray	1.24 A	A	906	957	Spike protein S2	Spike protein S2	-
2	pdb_00006lxt	6LXT	X-ray	2.90 A	A/B/C/D/E/F	910	988	Spike protein S2, Spike protein S2	-	-
3	pdb_00007c53	7C53	X-ray	2.28 A	A/B/C/D/E/F	910	975	Spike protein S2', pan-CoVs inhibitor EK1	-	-
4	pdb_00006x45	6X45	X-ray	2.20 A	A/B/C	912	966	Spike protein S2'	Spike protein S2'	-
5	pdb_00007rzq	7RZQ	EM	2.09 A	A/B/C	917	988	SARS-CoV-2 HR1 linked to a scaffold, Spike protein S2'	Spike protein S2'	-
6	pdb_00007rzr	7RZR	EM	2.27 A	A/B/C	917	988	SARS-CoV-2 HR1 D936Y linked to a scaffold, Spike protein S2'	Spike protein S2'	-
7	pdb_00007rzs	7RZS	EM	2.52 A	A/B/C	917	988	SARS-CoV-2 HR1 L938F linked to a scaffold, Spike protein S2'	Spike protein S2'	-
8	pdb_00007rzt	7RZT	EM	2.35 A	A/B/C	917	988	SARS-CoV-2 HR1 S940F linked to a scaffold, Spike protein S2'	Spike protein S2'	-
9	pdb_00007rzu	7RZU	EM	2.30 A	A/B/C	917	988	SARS-CoV-2 HR1 A942S linked to a scaffold, Spike protein S2'	Spike protein S2'	-
10	pdb_00007rzv	7RZV	EM	2.11 A	A/B/C	917	988	SARS-CoV-2 HR1 linked to a scaffold, Spike protein S2'	Spike protein S2'	-
11	pdb_00007tik	7TIK	EM	2.40 A	A/B/C	917	988	Ferritin, Dps family protein and Spike protein S2' chimera	Spike protein S2'	-
12	pdb_00008czi	8CZI	EM	2.22 A	A/B/C	917	988	Scaffolded Spike protein S2' HR1	Spike protein S2' HR2	-
13	pdb_00008fa2	8FA2	EM	2.82 A	A/B/C	917	988	Scaffolded Spike protein S2' HR1	Spike protein S2' 42G	-
14	pdb_00006m1v	6M1V	X-ray	1.50 A	A	917	966	Spike protein S2, Spike protein S2	-	-
15	pdb_00007r95	7R95	NMR	-	A	919	966	Spike protein S2	-	-
16	pdb_00008elh	8ELH	X-ray	1.85 A	C	919	927	Spike protein S2'	Heavy chain HLA-B*15:01	Beta-2-microglobulin
17	pdb_00007y8j	7Y8J	X-ray	1.03 A	A	950	955	Spike protein S2'	Heavy chain of 3D1	Light chain of 3D1
18	pdb_00008rbu	8RBU	X-ray	2.70 A	C	975	984	Spike protein S2'	HLA class I histocompatibility antigen	Beta-2-microglobulin
19	pdb_00008rcv	8RCV	X-ray	1.65 A	C	975	984	Spike protein S2'	HLA class I histocompatibility antigen B alpha chain	Beta-2-microglobulin
20	pdb_00008ref	8REF	X-ray	1.90 A	C	975	984	Spike protein S2'	HLA class I histocompatibility antigen B alpha chain	Beta-2-microglobulin
21	pdb_00008rh6	8RH6	X-ray	3.32 A	G/H/I	975	984	Spike protein S2'	HLA class I histocompatibility antigen	Beta-2-microglobulin
22	pdb_00008rhq	8RHQ	X-ray	2.00 A	G/H/I	975	984	Spike protein S2'	HLA class I histocompatibility antigen	Beta-2-microglobulin
23	pdb_00007sis	7SIS	X-ray	1.90 A	C	976	984	Spike protein S2' peptide VLNDILSRL	HLA class I histocompatibility antigen, A-2 alpha chain	Beta-2-microglobulin
24	pdb_00008rbv	8RBV	X-ray	1.80 A	C	976	984	SARS-CoV-2 Spike-derived peptide S976-984 S982A mutant	HLA class I antigen	Beta-2-microglobulin