SARS-CoV-2 Ligands Database

HR2+TM

Heptad Repeat 2 (HR2) is a region that also contains repeating patterns of seven amino acids (like HR1). It is located within the S2 subunit of the spike protein. HR2 plays a crucial role in the membrane fusion process. After the spike protein undergoes conformational changes during viral entry, HR2 interacts with HR1 (Heptad Repeat 1) to form a stable six-helix bundle structure. This structure is essential for bringing the viral and host cell membranes close together, allowing them to fuse.

The Transmembrane Domain (TM) is a segment of the spike protein that spans the viral membrane. It is typically located at the C-terminal end of the S2 subunit. The TM domain anchors the spike protein to the viral envelope and is essential for maintaining the structural integrity of the protein. It also plays a role in the final steps of the fusion process, stabilizing the post-fusion conformation.

№	Extended PDB ID	PDB ID	Method	Resolution	Chain	Start	End	Macromolecules	Ligand 1	Ligand 2	Ligand 3
1	pdb_00007nab	7NAB	X-ray	2.15 A	C/D	1140	1165	Spike protein S2	CV3-25 Fab Heavy Chain	CV3-25 Fab Light Chain	-
2	pdb_00007sjs	7SJS	X-ray	1.61 A	C	1140	1164	Stem helix peptide of Spike protein S2'	CC40.8 Fab heavy chain	CC40.8 Fab light chain	-
3	pdb_00008dgu	8DGU	X-ray	1.89 A	A	1140	1164	Spike protein S2'	Antibody CC25.106 Fab heavy chain	Antibody CC25.106 Fab light chain	-
4	pdb_00008tmy	8TMY	X-ray	3.07 A	M/N/S	1140	1164	Stem helix peptide of Spike protein S2'	Neutralizing antibody CHM-16 Heavy Chain	Neutralizing antibody CHM-16 Light Chain	-
5	pdb_00008dtr	8DTR	X-ray	1.50 A	G/J	1145	1159	Spike protein S2' stem helix peptide	COV30-14 heavy chain	COV30-14 light chain	-
6	pdb_00008dtx	8DTX	X-ray	1.60 A	G/I	1145	1159	Spike protein S2' stem helix peptide	COV89-22 heavy chain	COV89-22 light chain	-
7	pdb_00007s3n	7S3N	X-ray	1.90 A	A	1146	1164	Spike glycoprotein	Fab22 Heavy Chain	Fab22 Light Chain	-
8	pdb_00007m53	7M53	X-ray	1.40 A	A	1146	1161	Spike glycoprotein stem helix peptide	B6 antigen-binding (Fab) fragment heavy chain	B6 antigen-binding (Fab) fragment light chain	-
9	pdb_00007rnj	7RNJ	X-ray	2.67 A	B	1146	1159	Spike glycoprotein stem helix peptide	Monoclonal antibody S2P6 Fab light chain	Monoclonal antibody S2P6 Fab heavy chain	-
10	pdb_00008dtt	8DTT	X-ray	1.75 A	G/J	1148	1162	Spike protein S2' stem helix peptide	COV93-03 heavy chain	COV93-03 light chain	-
11	pdb_00007tcq	7TCQ	X-ray	2.02 A	C/D	1148	1157	Pegylated spike S2 peptide	Anti-SARS-CoV-2 antibody WS6 Fab heavy chain	Anti-SARS-CoV-2 antibody WS6 Fab light chain	Anti-SARS-CoV-2 antibody WS6 Fab light chain
12	pdb_00007raq	7RAQ	X-ray	1.74 A	P	1149	1167	Spike stem helix peptide	CV3-25 Fab Heavy Chain	CV3-25 Fab Light Chain	-
13	pdb_00007rzv	7RZV	EM	2.11 A	D/E/F	1157	1201	SARS-CoV-2 HR1 linked to a scaffold, Spike protein S2'	Spike protein S2'	-	-
14	pdb_00007tik	7TIK	EM	2.40 A	D/E/F	1157	1201	Ferritin, Dps family protein and Spike protein S2' chimera	Spike protein S2'	-	-
15	pdb_00008czi	8CZI	EM	2.22 A	D/E/F	1157	1201	Scaffolded Spike protein S2' HR1	Spike protein S2' HR2	-	-
16	pdb_00008fa1	8FA1	EM	2.51 A	D/E/F	1157	1201	Ferritin, Dps family protein and Spike protein S2' chimera	Spike protein S2' HR2	-	-
17	pdb_00008fa2	8FA2	EM	2.82 A	D/E/F	1157	1201	Scaffolded Spike protein S2' HR1	Spike protein S2' 42G	-	-
18	pdb_00006lxt	6LXT	X-ray	2.90 A	A/B/C/D	1162	1206	Spike protein S2, Spike protein S2	-	-	-
19	pdb_00007rzq	7RZQ	EM	2.09 A	D/E/F	1162	1201	SARS-CoV-2 HR1 linked to a scaffold, Spike protein S2'	Spike protein S2'	-	-
20	pdb_00007rzr	7RZR	EM	2.27 A	D/E/F	1162	1201	SARS-CoV-2 HR1 D936Y linked to a scaffold, Spike protein S2'	Spike protein S2'	-	-
21	pdb_00007rzs	7RZS	EM	2.52 A	D/E/F	1162	1201	SARS-CoV-2 HR1 L938F linked to a scaffold, Spike protein S2'	Spike protein S2'	-	-
22	pdb_00007rzt	7RZT	EM	2.35 A	D/E/F	1162	1201	SARS-CoV-2 HR1 S940F linked to a scaffold,Spike protein S2'	Spike protein S2'	-	-
23	pdb_00007rzu	7RZU	EM	2.30 A	D/E/F	1162	1201	SARS-CoV-2 HR1 A942S linked to a scaffold,Spike protein S2'	Spike protein S2'	-	-
24	pdb_00007zr2	7ZR2	X-ray	1.45 A	B	1163	1206	Spike protein S2', Chimeric protein mimic of SARS-CoV-2 Spike HR1	Spike protein S2'	-	-
25	pdb_00006lvn	6LVN	X-ray	2.47 A	A/B/C/D	1168	1203	Spike protein S2'	-	-	-
26	pdb_00006x45	6X45	X-ray	2.20 A	D/E/F	1168	1203	Spike protein S2'	Spike protein S2'	-	-
27	pdb_00007ek6	7EK6	X-ray	1.24 A	B	1175	1211	Spike protein S2	Spike protein S2	-	-
28	pdb_00007owx	7OWX	X-ray	1.93 A	A/B/C/D	1177	1203	Spike protein S2	-	-	-
29	pdb_00007u1r	7U1R	X-ray	1.80 A	C	1185	1193	Spike protein S2' peptide	HLA class I antigen	Beta-2-microglobulin	-
30	pdb_00007ejl	7EJL	X-ray	1.89 A	C	1208	1216	9-mer peptide from the HCoV spike protein	MHC class I antigen	Beta-2-microglobulin	-
31	pdb_00008hn4	8HN4	X-ray	2.85 A	E	1208	1216	-	MHC class I antigen	Beta-2-microglobulin	SARS-CoV-2 T-cell epitope QYIKWPWYI
32	pdb_00007ur1	7UR1	X-ray	2.17 A	C	1215	1224	SARS-CoV-2 Spike-derived peptide S1215-1224 (YIWLGFIAGL)	HLA class I antigen	Beta-2-microglobulin	-
33	pdb_00007lc8	7LC8	NMR	-	A/B/C	1217	1237	Spike protein S2'	-	-	-
34	pdb_00008ens	8ENS	X-ray	1.45 A	C	1267	1273	Spike tail hepta-peptide	Coatomer subunit beta'	-	-
35	pdb_00008enw	8ENW	X-ray	1.45 A	C/D	1267	1272	Clientized spike tail peptide	Coatomer subunit beta'	-	-
36	pdb_00008enx	8ENX	X-ray	1.80 A	C	1267	1272	Clientized spike tail heptapeptide	Coatomer subunit beta'	-	-
37	pdb_00008hqt	8HQT	X-ray	1.80 A	B	1268	1273	SARS-CoV-2 Spike KxHxx motif	Coatomer subunit beta'	-	-