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Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

8ZC6

SARS-CoV-2 Omicron BA.4 spike trimer (6P) in complex with D1F6 Fab, head-to-head aggregate

Functional Information from PROSITE/UniProt

site_id	PS00290
Number of Residues	7
Details	IG_MHC Immunoglobulins and major histocompatibility complex proteins signature. YSCQVTH

Chain	Residue	Details
G	TYR202-HIS208
H	TYR208-HIS214

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	6
Details	SITE: Cleavage; by host furin => ECO:0000255\|HAMAP-Rule:MF_04099, ECO:0000269\|PubMed:32142651, ECO:0000269\|PubMed:32362314, ECO:0000269\|PubMed:32703818, ECO:0000269\|PubMed:34159616

Chain	Residue	Details
A	ALA694
B	ALA694
C	ALA694
D	ALA694
E	ALA694
F	ALA694

site_id	SWS_FT_FI2
Number of Residues	6
Details	SITE: Cleavage; by host TMPRSS2 or CTSL => ECO:0000255\|HAMAP-Rule:MF_04099, ECO:0000269\|PubMed:32703818, ECO:0000269\|PubMed:34159616

Chain	Residue	Details
A	ASN824
B	ASN824
C	ASN824
D	ASN824
E	ASN824
F	ASN824

site_id	SWS_FT_FI3
Number of Residues	18
Details	CARBOHYD: N-linked (GlcNAc...) (complex) asparagine; by host => ECO:0000255\|HAMAP-Rule:MF_04099, ECO:0000269\|PubMed:32366695, ECO:0000269\|PubMed:32979942

Chain	Residue	Details
A	ASN20
D	ASN20
D	GLY1167
D	GLU1182
E	ASN20
E	GLY1167
E	GLU1182
F	ASN20
F	GLY1167
F	GLU1182
A	GLY1167
A	GLU1182
B	ASN20
B	GLY1167
B	GLU1182
C	ASN20
C	GLY1167
C	GLU1182

site_id	SWS_FT_FI4
Number of Residues	30
Details	CARBOHYD: N-linked (GlcNAc...) (hybrid) asparagine; by host => ECO:0000255\|HAMAP-Rule:MF_04099, ECO:0000269\|PubMed:32155444, ECO:0000269\|PubMed:32363391, ECO:0000269\|PubMed:32366695, ECO:0000269\|PubMed:32979942

Chain	Residue	Details
A	TRP64
B	HIS1083
C	TRP64
C	VAL127
C	ILE726
C	SER810
C	HIS1083
D	TRP64
D	VAL127
D	ILE726
D	SER810
A	VAL127
D	HIS1083
E	TRP64
E	VAL127
E	ILE726
E	SER810
E	HIS1083
F	TRP64
F	VAL127
F	ILE726
F	SER810
A	ILE726
F	HIS1083
A	SER810
A	HIS1083
B	TRP64
B	VAL127
B	ILE726
B	SER810

site_id	SWS_FT_FI5
Number of Residues	18
Details	CARBOHYD: N-linked (GlcNAc...) (complex) asparagine; by host => ECO:0000255\|HAMAP-Rule:MF_04099, ECO:0000269\|PubMed:32363391, ECO:0000269\|PubMed:32366695, ECO:0000269\|PubMed:32979942

Chain	Residue	Details
A	PHE79
D	PHE79
D	GLU154
D	LEU1203
E	PHE79
E	GLU154
E	LEU1203
F	PHE79
F	GLU154
F	LEU1203
A	GLU154
A	LEU1203
B	PHE79
B	GLU154
B	LEU1203
C	PHE79
C	GLU154
C	LEU1203

site_id	SWS_FT_FI6
Number of Residues	42
Details	CARBOHYD: N-linked (GlcNAc...) (complex) asparagine; by host => ECO:0000255\|HAMAP-Rule:MF_04099, ECO:0000269\|PubMed:32155444, ECO:0000269\|PubMed:32363391, ECO:0000269\|PubMed:32366695, ECO:0000269\|PubMed:32979942

Chain	Residue	Details
A	TYR170
B	CYS336
B	ALA348
B	PRO621
B	CYS662
B	ARG1107
C	TYR170
C	ASP287
C	CYS336
C	ALA348
C	PRO621
A	ASP287
C	CYS662
C	ARG1107
D	TYR170
D	ASP287
D	CYS336
D	ALA348
D	PRO621
D	CYS662
D	ARG1107
E	TYR170
A	CYS336
E	ASP287
E	CYS336
E	ALA348
E	PRO621
E	CYS662
E	ARG1107
F	TYR170
F	ASP287
F	CYS336
F	ALA348
A	ALA348
F	PRO621
F	CYS662
F	ARG1107
A	PRO621
A	CYS662
A	ARG1107
B	TYR170
B	ASP287

site_id	SWS_FT_FI7
Number of Residues	12
Details	CARBOHYD: N-linked (GlcNAc...) (high mannose) asparagine; by host => ECO:0000255\|HAMAP-Rule:MF_04099, ECO:0000269\|PubMed:32155444, ECO:0000269\|PubMed:32363391, ECO:0000269\|PubMed:32366695, ECO:0000269\|PubMed:32979942

Chain	Residue	Details
A	GLN239
E	PHE718
F	GLN239
F	PHE718
A	PHE718
B	GLN239
B	PHE718
C	GLN239
C	PHE718
D	GLN239
D	PHE718
E	GLN239

site_id	SWS_FT_FI8
Number of Residues	6
Details	CARBOHYD: O-linked (GalNAc) threonine; by host => ECO:0000269\|PubMed:32363391

Chain	Residue	Details
A	ARG328
B	ARG328
C	ARG328
D	ARG328
E	ARG328
F	ARG328

site_id	SWS_FT_FI9
Number of Residues	6
Details	CARBOHYD: O-linked (HexNAc...) serine; by host => ECO:0000269\|PubMed:32363391

Chain	Residue	Details
A	PRO330
B	PRO330
C	PRO330
D	PRO330
E	PRO330
F	PRO330

site_id	SWS_FT_FI10
Number of Residues	6
Details	CARBOHYD: N-linked (GlcNAc...) (hybrid) asparagine; by host => ECO:0000255\|HAMAP-Rule:MF_04099, ECO:0000269\|PubMed:32155444, ECO:0000269\|PubMed:32366695, ECO:0000269\|PubMed:32979942

Chain	Residue	Details
A	VAL608
B	VAL608
C	VAL608
D	VAL608
E	VAL608
F	VAL608

site_id	SWS_FT_FI11
Number of Residues	12
Details	CARBOHYD: O-linked (GlcNAc...) threonine; by host GALNT1 => ECO:0000269\|PubMed:34732583

Chain	Residue	Details
A	ARG685
E	VAL687
F	ARG685
F	VAL687
A	VAL687
B	ARG685
B	VAL687
C	ARG685
C	VAL687
D	ARG685
D	VAL687
E	ARG685

site_id	SWS_FT_FI12
Number of Residues	6
Details	CARBOHYD: N-linked (GlcNAc...) (complex) asparagine; by host => ECO:0000255\|HAMAP-Rule:MF_04099, ECO:0000269\|PubMed:32155444, ECO:0000269\|PubMed:32366695, ECO:0000269\|PubMed:32979942

Chain	Residue	Details
A	PRO1143
B	PRO1143
C	PRO1143
D	PRO1143
E	PRO1143
F	PRO1143

221716

PDB entries from 2024-06-26

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