Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

6HBY

HLA class II peptide flanking residues tune the immunogenicity of a human tumor-derived epitope

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0006955	biological_process	immune response
A	0016020	cellular_component	membrane
A	0019882	biological_process	antigen processing and presentation
A	0042613	cellular_component	MHC class II protein complex
B	0006955	biological_process	immune response
B	0016020	cellular_component	membrane
B	0019882	biological_process	antigen processing and presentation
B	0042613	cellular_component	MHC class II protein complex
D	0006955	biological_process	immune response
D	0016020	cellular_component	membrane
D	0019882	biological_process	antigen processing and presentation
D	0042613	cellular_component	MHC class II protein complex
E	0006955	biological_process	immune response
E	0016020	cellular_component	membrane
E	0019882	biological_process	antigen processing and presentation
E	0042613	cellular_component	MHC class II protein complex

Functional Information from PDB Data

site_id	AC1
Number of Residues	5
Details	binding site for residue EDO A 201

Chain	Residue
A	TYR79
A	PRO81
E	PHE132
E	GLY135
E	THR172

site_id	AC2
Number of Residues	2
Details	binding site for residue EDO A 202

Chain	Residue
A	THR83
A	ASN84

site_id	AC3
Number of Residues	5
Details	binding site for residue EDO A 203

Chain	Residue
A	HOH319
B	THR3
B	ARG4
A	ASN84
A	TRP168

site_id	AC4
Number of Residues	7
Details	binding site for residue EDO A 204

Chain	Residue
A	ASP25
A	GLY28
A	PRO139
A	ARG140
A	GLU141
A	ARG146
B	HOH319

site_id	AC5
Number of Residues	4
Details	binding site for residue EDO A 205

Chain	Residue
A	TRP43
A	SER53
A	PHE54
C	ARG4

site_id	AC6
Number of Residues	4
Details	binding site for residue PO4 A 206

Chain	Residue
A	LYS111
A	ARG140
A	HOH350
E	ARG39

site_id	AC7
Number of Residues	3
Details	binding site for residue EDO B 201

Chain	Residue
B	ARG39
B	ASP41
B	HOH318

site_id	AC8
Number of Residues	4
Details	binding site for residue EDO B 202

Chain	Residue
B	TYR60
B	GLN64
C	LEU13
C	ASN14

site_id	AC9
Number of Residues	8
Details	binding site for residue EDO B 203

Chain	Residue
A	ILE82
A	THR83
B	TYR32
B	ASN33
B	GLN34
B	GLU35
B	HOH306
B	HOH349

site_id	AD1
Number of Residues	5
Details	binding site for residue EDO B 204

Chain	Residue
B	THR77
B	GLN110
B	HIS111
B	HOH341
C	GLU9

site_id	AD2
Number of Residues	4
Details	binding site for residue EDO B 205

Chain	Residue
B	GLN70
B	ARG71
B	GLN110
C	LEU10

site_id	AD3
Number of Residues	4
Details	binding site for residue EDO B 206

Chain	Residue
B	ARG23
B	VAL24
B	ARG80
E	LYS139

site_id	AD4
Number of Residues	4
Details	binding site for residue EDO B 207

Chain	Residue
B	HIS111
B	HIS112
B	PRO165
B	HOH330

site_id	AD5
Number of Residues	4
Details	binding site for residue EDO B 208

Chain	Residue
A	ASN94
A	TYR150
B	ASP152
B	HOH327

site_id	AD6
Number of Residues	6
Details	binding site for residue EDO B 209

Chain	Residue
A	PHE26
A	ASP27
B	TYR123
B	PRO124
B	GLY125
B	PHE155

site_id	AD7
Number of Residues	3
Details	binding site for residue EDO B 210

Chain	Residue
A	PHE51
B	VAL85
B	SER88

site_id	AD8
Number of Residues	3
Details	binding site for residue EDO B 211

Chain	Residue
B	ARG39
D	LYS111
D	ARG140

site_id	AD9
Number of Residues	5
Details	binding site for residue PO4 B 212

Chain	Residue
B	GLU46
B	ARG72
E	GLY141
E	VAL143
E	GLU162

site_id	AE1
Number of Residues	6
Details	binding site for residue PO4 B 213

Chain	Residue
B	ALA49
B	VAL50
B	THR51
B	GLU52
B	ARG55
D	GLU88

site_id	AE2
Number of Residues	5
Details	binding site for residue EDO D 201

Chain	Residue
D	THR41
D	TRP43
D	SER53
D	PHE54
F	ARG4

site_id	AE3
Number of Residues	5
Details	binding site for residue EDO D 202

Chain	Residue
D	ILE82
D	ASN84
E	THR3
E	ARG4
E	ARG6

site_id	AE4
Number of Residues	5
Details	binding site for residue EDO D 203

Chain	Residue
E	ILE148
E	GLN149
D	PHE108
D	ARG146
E	LEU147

site_id	AE5
Number of Residues	7
Details	binding site for residue EDO D 204

Chain	Residue
D	ILE8
D	ASP25
D	GLY28
D	PRO139
D	ARG140
D	GLU141
E	HOH311

site_id	AE6
Number of Residues	5
Details	binding site for residue EDO E 201

Chain	Residue
E	GLN70
E	ARG71
E	LEU109
E	GLN110
E	HOH326

site_id	AE7
Number of Residues	7
Details	binding site for residue EDO E 202

Chain	Residue
E	THR77
E	GLN110
E	HIS111
E	HOH326
E	HOH341
F	ALA8
F	GLU9

site_id	AE8
Number of Residues	6
Details	binding site for residue EDO E 203

Chain	Residue
D	ILE82
D	THR83
E	ASN33
E	GLN34
E	GLU35
E	HOH306

site_id	AE9
Number of Residues	4
Details	binding site for residue EDO E 204

Chain	Residue
D	ASN94
D	TYR150
E	ASP152
E	HOH321

site_id	AF1
Number of Residues	6
Details	binding site for residue EDO E 205

Chain	Residue
E	GLN34
E	GLU35
E	GLU36
E	VAL50
E	THR51
E	HOH316

site_id	AF2
Number of Residues	2
Details	binding site for residue PO4 E 206

Chain	Residue
E	HIS111
E	HIS112

site_id	AF3
Number of Residues	4
Details	binding site for residue PO4 E 207

Chain	Residue
E	PRO178
E	SER179
E	VAL180
E	HOH313

Functional Information from PROSITE/UniProt

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

Chain	Residue	Details
A	TYR161-HIS167
B	TYR171-HIS177
D	TYR161-HIS167

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	360
Details	Domain: {"description":"Ig-like C1-type"}

Chain

Residue

Details

site_id	SWS_FT_FI2
Number of Residues	186
Details	Region: {"description":"Alpha-2"}

Chain

Residue

Details

site_id	SWS_FT_FI3
Number of Residues	2
Details	Site: {"description":"Self- and pathogen-derived peptide antigen","evidences":[{"source":"PubMed","id":"17583734","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"21115828","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"23260142","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"8145819","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"4GBX","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI4
Number of Residues	4
Details	Site: {"description":"Self-peptide antigen","evidences":[{"source":"PubMed","id":"31619516","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI5
Number of Residues	2
Details	Site: {"description":"Self- and pathogen-derived peptide antigen","evidences":[{"source":"PubMed","id":"21115828","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"8145819","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI6
Number of Residues	2
Details	Site: {"description":"Self- and pathogen-derived peptide antigen","evidences":[{"source":"PubMed","id":"17583734","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"21115828","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"31619516","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"8145819","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI7
Number of Residues	2
Details	Site: {"description":"Pathogen-derived peptide antigen","evidences":[{"source":"PubMed","id":"23260142","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"4GBX","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI8
Number of Residues	2
Details	Site: {"description":"Self- and pathogen-derived peptide antigen","evidences":[{"source":"PubMed","id":"17583734","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"21115828","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"23260142","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"31619516","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"8145819","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"4GBX","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI9
Number of Residues	2
Details	Site: {"description":"Pathogen-derived peptide antigen","evidences":[{"source":"PubMed","id":"17583734","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"21115828","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"23260142","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"8145819","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"4FQX","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4GBX","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI10
Number of Residues	2
Details	Site: {"description":"Self- and pathogen-derived peptide antigen","evidences":[{"source":"PubMed","id":"17583734","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"23260142","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"31619516","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"8145819","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"4FQX","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4GBX","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI11
Number of Residues	4
Details	Glycosylation: {"description":"N-linked (GlcNAc...) asparagine","evidences":[{"source":"PubMed","id":"19159218","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"7477400","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI12
Number of Residues	188
Details	Region: {"description":"Beta-1"}

Chain

Residue

Details

site_id	SWS_FT_FI13
Number of Residues	8
Details	Binding site: {"evidences":[{"source":"PubMed","id":"31619516","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"8145819","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI14
Number of Residues	2
Details	Binding site: {"evidences":[{"source":"PubMed","id":"8145819","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI15
Number of Residues	2
Details	Glycosylation: {"description":"N-linked (GlcNAc...) asparagine","evidences":[{"source":"PubMed","id":"19303388","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"24190431","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI16
Number of Residues	2
Details	Glycosylation: {"description":"N-linked (GlcNAc...) asparagine","evidences":[{"source":"PubMed","id":"19159218","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

		Sequence (fasta)
		PDBx/mmCIF
		PDBML format (no-atom)
		PDB format (full)
		Validation report (PDF)
		EDMap 2fo-fc (MTZ)