Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

5D2N

Crystal structure of C25-NLV-HLA-A2 complex

Functional Information from GO Data

Chain	GOid	namespace	contents
B	0000139	cellular_component	Golgi membrane
B	0002376	biological_process	immune system process
B	0002474	biological_process	antigen processing and presentation of peptide antigen via MHC class I
B	0002477	biological_process	antigen processing and presentation of exogenous peptide antigen via MHC class Ib
B	0002502	biological_process	peptide antigen assembly with MHC class I protein complex
B	0002503	biological_process	peptide antigen assembly with MHC class II protein complex
B	0002715	biological_process	regulation of natural killer cell mediated immunity
B	0002726	biological_process	positive regulation of T cell cytokine production
B	0005198	molecular_function	structural molecule activity
B	0005515	molecular_function	protein binding
B	0005576	cellular_component	extracellular region
B	0005615	cellular_component	extracellular space
B	0005765	cellular_component	lysosomal membrane
B	0005783	cellular_component	endoplasmic reticulum
B	0005788	cellular_component	endoplasmic reticulum lumen
B	0005794	cellular_component	Golgi apparatus
B	0005886	cellular_component	plasma membrane
B	0005925	cellular_component	focal adhesion
B	0006879	biological_process	intracellular iron ion homeostasis
B	0006955	biological_process	immune response
B	0007608	biological_process	sensory perception of smell
B	0007611	biological_process	learning or memory
B	0009897	cellular_component	external side of plasma membrane
B	0009986	cellular_component	cell surface
B	0010038	biological_process	response to metal ion
B	0012507	cellular_component	ER to Golgi transport vesicle membrane
B	0016020	cellular_component	membrane
B	0019885	biological_process	antigen processing and presentation of endogenous peptide antigen via MHC class I
B	0019886	biological_process	antigen processing and presentation of exogenous peptide antigen via MHC class II
B	0023026	molecular_function	MHC class II protein complex binding
B	0030670	cellular_component	phagocytic vesicle membrane
B	0031901	cellular_component	early endosome membrane
B	0031902	cellular_component	late endosome membrane
B	0031905	cellular_component	early endosome lumen
B	0032398	cellular_component	MHC class Ib protein complex
B	0033572	biological_process	transferrin transport
B	0034756	biological_process	regulation of iron ion transport
B	0034757	biological_process	negative regulation of iron ion transport
B	0035580	cellular_component	specific granule lumen
B	0042605	molecular_function	peptide antigen binding
B	0042612	cellular_component	MHC class I protein complex
B	0042613	cellular_component	MHC class II protein complex
B	0042802	molecular_function	identical protein binding
B	0042803	molecular_function	protein homodimerization activity
B	0042824	cellular_component	MHC class I peptide loading complex
B	0048260	biological_process	positive regulation of receptor-mediated endocytosis
B	0048261	biological_process	negative regulation of receptor-mediated endocytosis
B	0050680	biological_process	negative regulation of epithelial cell proliferation
B	0050768	biological_process	negative regulation of neurogenesis
B	0050778	biological_process	positive regulation of immune response
B	0050870	biological_process	positive regulation of T cell activation
B	0051289	biological_process	protein homotetramerization
B	0055038	cellular_component	recycling endosome membrane
B	0070062	cellular_component	extracellular exosome
B	0071281	biological_process	cellular response to iron ion
B	0071316	biological_process	cellular response to nicotine
B	1904724	cellular_component	tertiary granule lumen
B	1990000	biological_process	amyloid fibril formation
B	1990712	cellular_component	HFE-transferrin receptor complex
B	2000774	biological_process	positive regulation of cellular senescence
B	2000978	biological_process	negative regulation of forebrain neuron differentiation
L	0000139	cellular_component	Golgi membrane
L	0002376	biological_process	immune system process
L	0002474	biological_process	antigen processing and presentation of peptide antigen via MHC class I
L	0002477	biological_process	antigen processing and presentation of exogenous peptide antigen via MHC class Ib
L	0002502	biological_process	peptide antigen assembly with MHC class I protein complex
L	0002503	biological_process	peptide antigen assembly with MHC class II protein complex
L	0002715	biological_process	regulation of natural killer cell mediated immunity
L	0002726	biological_process	positive regulation of T cell cytokine production
L	0005198	molecular_function	structural molecule activity
L	0005515	molecular_function	protein binding
L	0005576	cellular_component	extracellular region
L	0005615	cellular_component	extracellular space
L	0005765	cellular_component	lysosomal membrane
L	0005783	cellular_component	endoplasmic reticulum
L	0005788	cellular_component	endoplasmic reticulum lumen
L	0005794	cellular_component	Golgi apparatus
L	0005886	cellular_component	plasma membrane
L	0005925	cellular_component	focal adhesion
L	0006879	biological_process	intracellular iron ion homeostasis
L	0006955	biological_process	immune response
L	0007608	biological_process	sensory perception of smell
L	0007611	biological_process	learning or memory
L	0009897	cellular_component	external side of plasma membrane
L	0009986	cellular_component	cell surface
L	0010038	biological_process	response to metal ion
L	0012507	cellular_component	ER to Golgi transport vesicle membrane
L	0016020	cellular_component	membrane
L	0019885	biological_process	antigen processing and presentation of endogenous peptide antigen via MHC class I
L	0019886	biological_process	antigen processing and presentation of exogenous peptide antigen via MHC class II
L	0023026	molecular_function	MHC class II protein complex binding
L	0030670	cellular_component	phagocytic vesicle membrane
L	0031901	cellular_component	early endosome membrane
L	0031902	cellular_component	late endosome membrane
L	0031905	cellular_component	early endosome lumen
L	0032398	cellular_component	MHC class Ib protein complex
L	0033572	biological_process	transferrin transport
L	0034756	biological_process	regulation of iron ion transport
L	0034757	biological_process	negative regulation of iron ion transport
L	0035580	cellular_component	specific granule lumen
L	0042605	molecular_function	peptide antigen binding
L	0042612	cellular_component	MHC class I protein complex
L	0042613	cellular_component	MHC class II protein complex
L	0042802	molecular_function	identical protein binding
L	0042803	molecular_function	protein homodimerization activity
L	0042824	cellular_component	MHC class I peptide loading complex
L	0048260	biological_process	positive regulation of receptor-mediated endocytosis
L	0048261	biological_process	negative regulation of receptor-mediated endocytosis
L	0050680	biological_process	negative regulation of epithelial cell proliferation
L	0050768	biological_process	negative regulation of neurogenesis
L	0050778	biological_process	positive regulation of immune response
L	0050870	biological_process	positive regulation of T cell activation
L	0051289	biological_process	protein homotetramerization
L	0055038	cellular_component	recycling endosome membrane
L	0070062	cellular_component	extracellular exosome
L	0071281	biological_process	cellular response to iron ion
L	0071316	biological_process	cellular response to nicotine
L	1904724	cellular_component	tertiary granule lumen
L	1990000	biological_process	amyloid fibril formation
L	1990712	cellular_component	HFE-transferrin receptor complex
L	2000774	biological_process	positive regulation of cellular senescence
L	2000978	biological_process	negative regulation of forebrain neuron differentiation

Functional Information from PDB Data

site_id	AC1
Number of Residues	5
Details	binding site for residue IMD C 301

Chain	Residue
C	ALA2
C	LYS3
C	THR4
C	ARG97
C	GLY99

site_id	AC2
Number of Residues	4
Details	binding site for residue IMD A 301

Chain	Residue
A	PHE8
A	ASP29
A	ASP30
B	TYR63

site_id	AC3
Number of Residues	5
Details	binding site for residue IMD A 302

Chain	Residue
A	ASP196
A	SER251
E	ASN164
E	LYS166
L	ILE1

Functional Information from PROSITE/UniProt

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

Chain	Residue	Details
L	TYR78-HIS84
H	TYR257-HIS263

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	172
Details	Domain: {"description":"Ig-like C1-type","evidences":[{"evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI2
Number of Residues	182
Details	Region: {"description":"Alpha-2","evidences":[{"evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI3
Number of Residues	182
Details	Region: {"description":"Alpha-3","evidences":[{"evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI4
Number of Residues	12
Details	Binding site: {"evidences":[{"source":"PubMed","id":"21943705","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI5
Number of Residues	4
Details	Binding site: {"evidences":[{"source":"PubMed","id":"21543847","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI6
Number of Residues	2
Details	Modified residue: {"description":"Sulfotyrosine","evidences":[{"evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI7
Number of Residues	2
Details	Glycosylation: {"description":"N-linked (GlcNAc...) asparagine","evidences":[{"source":"PubMed","id":"19159218","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI8
Number of Residues	176
Details	Domain: {"description":"Ig-like C1-type"}

Chain

Residue

Details

site_id	SWS_FT_FI9
Number of Residues	2
Details	Modified residue: {"description":"Pyrrolidone carboxylic acid; in form pI 5.3","evidences":[{"source":"PubMed","id":"7554280","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI10
Number of Residues	2
Details	Glycosylation: {"description":"N-linked (Glc) (glycation) isoleucine; in hemodialysis-associated amyloidosis","evidences":[{"source":"PubMed","id":"7918443","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI11
Number of Residues	12
Details	Glycosylation: {"description":"N-linked (Glc) (glycation) lysine; in vitro","evidences":[{"source":"PubMed","id":"7918443","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

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