5KD7

Crystal Structure of Murine MHC-I H-2Dd in complex with Murine Beta2-Microglobulin and a Variant of Peptide (PV9) of HIV gp120 MN Isolate (IGPGRAFYV)

Functional Information from GO Data

Chain	GOid	namespace	contents
B	0001916	biological_process	positive regulation of T cell mediated cytotoxicity
B	0002237	biological_process	response to molecule of bacterial origin
B	0002376	biological_process	immune system process
B	0002474	biological_process	antigen processing and presentation of peptide antigen via MHC class I
B	0002481	biological_process	antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent
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	0002726	biological_process	positive regulation of T cell cytokine production
B	0003254	biological_process	regulation of membrane depolarization
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	0005794	cellular_component	Golgi apparatus
B	0005829	cellular_component	cytosol
B	0005886	cellular_component	plasma membrane
B	0006826	biological_process	iron ion transport
B	0006879	biological_process	intracellular iron ion homeostasis
B	0006955	biological_process	immune response
B	0006968	biological_process	cellular defense 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	0010038	biological_process	response to metal ion
B	0010977	biological_process	negative regulation of neuron projection development
B	0019731	biological_process	antibacterial humoral response
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	0031902	cellular_component	late endosome membrane
B	0033077	biological_process	T cell differentiation in thymus
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	0042026	biological_process	protein refolding
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	0045087	biological_process	innate immune response
B	0045646	biological_process	regulation of erythrocyte differentiation
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	0050829	biological_process	defense response to Gram-negative bacterium
B	0050830	biological_process	defense response to Gram-positive bacterium
B	0050870	biological_process	positive regulation of T cell activation
B	0051289	biological_process	protein homotetramerization
B	0060586	biological_process	multicellular organismal-level iron ion homeostasis
B	0061844	biological_process	antimicrobial humoral immune response mediated by antimicrobial peptide
B	0071222	biological_process	cellular response to lipopolysaccharide
B	0071281	biological_process	cellular response to iron ion
B	0071283	biological_process	cellular response to iron(III) ion
B	0071316	biological_process	cellular response to nicotine
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
D	0001916	biological_process	positive regulation of T cell mediated cytotoxicity
D	0002237	biological_process	response to molecule of bacterial origin
D	0002376	biological_process	immune system process
D	0002474	biological_process	antigen processing and presentation of peptide antigen via MHC class I
D	0002481	biological_process	antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent
D	0002502	biological_process	peptide antigen assembly with MHC class I protein complex
D	0002503	biological_process	peptide antigen assembly with MHC class II protein complex
D	0002726	biological_process	positive regulation of T cell cytokine production
D	0003254	biological_process	regulation of membrane depolarization
D	0005198	molecular_function	structural molecule activity
D	0005515	molecular_function	protein binding
D	0005576	cellular_component	extracellular region
D	0005615	cellular_component	extracellular space
D	0005765	cellular_component	lysosomal membrane
D	0005794	cellular_component	Golgi apparatus
D	0005829	cellular_component	cytosol
D	0005886	cellular_component	plasma membrane
D	0006826	biological_process	iron ion transport
D	0006879	biological_process	intracellular iron ion homeostasis
D	0006955	biological_process	immune response
D	0006968	biological_process	cellular defense response
D	0007608	biological_process	sensory perception of smell
D	0007611	biological_process	learning or memory
D	0009897	cellular_component	external side of plasma membrane
D	0010038	biological_process	response to metal ion
D	0010977	biological_process	negative regulation of neuron projection development
D	0019731	biological_process	antibacterial humoral response
D	0019885	biological_process	antigen processing and presentation of endogenous peptide antigen via MHC class I
D	0019886	biological_process	antigen processing and presentation of exogenous peptide antigen via MHC class II
D	0023026	molecular_function	MHC class II protein complex binding
D	0030670	cellular_component	phagocytic vesicle membrane
D	0031902	cellular_component	late endosome membrane
D	0033077	biological_process	T cell differentiation in thymus
D	0033572	biological_process	transferrin transport
D	0034756	biological_process	regulation of iron ion transport
D	0034757	biological_process	negative regulation of iron ion transport
D	0042026	biological_process	protein refolding
D	0042605	molecular_function	peptide antigen binding
D	0042612	cellular_component	MHC class I protein complex
D	0042613	cellular_component	MHC class II protein complex
D	0042802	molecular_function	identical protein binding
D	0042803	molecular_function	protein homodimerization activity
D	0042824	cellular_component	MHC class I peptide loading complex
D	0045087	biological_process	innate immune response
D	0045646	biological_process	regulation of erythrocyte differentiation
D	0048260	biological_process	positive regulation of receptor-mediated endocytosis
D	0048261	biological_process	negative regulation of receptor-mediated endocytosis
D	0050680	biological_process	negative regulation of epithelial cell proliferation
D	0050768	biological_process	negative regulation of neurogenesis
D	0050778	biological_process	positive regulation of immune response
D	0050829	biological_process	defense response to Gram-negative bacterium
D	0050830	biological_process	defense response to Gram-positive bacterium
D	0050870	biological_process	positive regulation of T cell activation
D	0051289	biological_process	protein homotetramerization
D	0060586	biological_process	multicellular organismal-level iron ion homeostasis
D	0061844	biological_process	antimicrobial humoral immune response mediated by antimicrobial peptide
D	0071222	biological_process	cellular response to lipopolysaccharide
D	0071281	biological_process	cellular response to iron ion
D	0071283	biological_process	cellular response to iron(III) ion
D	0071316	biological_process	cellular response to nicotine
D	1990000	biological_process	amyloid fibril formation
D	1990712	cellular_component	HFE-transferrin receptor complex
D	2000774	biological_process	positive regulation of cellular senescence
D	2000978	biological_process	negative regulation of forebrain neuron differentiation
G	0001916	biological_process	positive regulation of T cell mediated cytotoxicity
G	0002237	biological_process	response to molecule of bacterial origin
G	0002376	biological_process	immune system process
G	0002474	biological_process	antigen processing and presentation of peptide antigen via MHC class I
G	0002481	biological_process	antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent
G	0002502	biological_process	peptide antigen assembly with MHC class I protein complex
G	0002503	biological_process	peptide antigen assembly with MHC class II protein complex
G	0002726	biological_process	positive regulation of T cell cytokine production
G	0003254	biological_process	regulation of membrane depolarization
G	0005198	molecular_function	structural molecule activity
G	0005515	molecular_function	protein binding
G	0005576	cellular_component	extracellular region
G	0005615	cellular_component	extracellular space
G	0005765	cellular_component	lysosomal membrane
G	0005794	cellular_component	Golgi apparatus
G	0005829	cellular_component	cytosol
G	0005886	cellular_component	plasma membrane
G	0006826	biological_process	iron ion transport
G	0006879	biological_process	intracellular iron ion homeostasis
G	0006955	biological_process	immune response
G	0006968	biological_process	cellular defense response
G	0007608	biological_process	sensory perception of smell
G	0007611	biological_process	learning or memory
G	0009897	cellular_component	external side of plasma membrane
G	0010038	biological_process	response to metal ion
G	0010977	biological_process	negative regulation of neuron projection development
G	0019731	biological_process	antibacterial humoral response
G	0019885	biological_process	antigen processing and presentation of endogenous peptide antigen via MHC class I
G	0019886	biological_process	antigen processing and presentation of exogenous peptide antigen via MHC class II
G	0023026	molecular_function	MHC class II protein complex binding
G	0030670	cellular_component	phagocytic vesicle membrane
G	0031902	cellular_component	late endosome membrane
G	0033077	biological_process	T cell differentiation in thymus
G	0033572	biological_process	transferrin transport
G	0034756	biological_process	regulation of iron ion transport
G	0034757	biological_process	negative regulation of iron ion transport
G	0042026	biological_process	protein refolding
G	0042605	molecular_function	peptide antigen binding
G	0042612	cellular_component	MHC class I protein complex
G	0042613	cellular_component	MHC class II protein complex
G	0042802	molecular_function	identical protein binding
G	0042803	molecular_function	protein homodimerization activity
G	0042824	cellular_component	MHC class I peptide loading complex
G	0045087	biological_process	innate immune response
G	0045646	biological_process	regulation of erythrocyte differentiation
G	0048260	biological_process	positive regulation of receptor-mediated endocytosis
G	0048261	biological_process	negative regulation of receptor-mediated endocytosis
G	0050680	biological_process	negative regulation of epithelial cell proliferation
G	0050768	biological_process	negative regulation of neurogenesis
G	0050778	biological_process	positive regulation of immune response
G	0050829	biological_process	defense response to Gram-negative bacterium
G	0050830	biological_process	defense response to Gram-positive bacterium
G	0050870	biological_process	positive regulation of T cell activation
G	0051289	biological_process	protein homotetramerization
G	0060586	biological_process	multicellular organismal-level iron ion homeostasis
G	0061844	biological_process	antimicrobial humoral immune response mediated by antimicrobial peptide
G	0071222	biological_process	cellular response to lipopolysaccharide
G	0071281	biological_process	cellular response to iron ion
G	0071283	biological_process	cellular response to iron(III) ion
G	0071316	biological_process	cellular response to nicotine
G	1990000	biological_process	amyloid fibril formation
G	1990712	cellular_component	HFE-transferrin receptor complex
G	2000774	biological_process	positive regulation of cellular senescence
G	2000978	biological_process	negative regulation of forebrain neuron differentiation
J	0001916	biological_process	positive regulation of T cell mediated cytotoxicity
J	0002237	biological_process	response to molecule of bacterial origin
J	0002376	biological_process	immune system process
J	0002474	biological_process	antigen processing and presentation of peptide antigen via MHC class I
J	0002481	biological_process	antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent
J	0002502	biological_process	peptide antigen assembly with MHC class I protein complex
J	0002503	biological_process	peptide antigen assembly with MHC class II protein complex
J	0002726	biological_process	positive regulation of T cell cytokine production
J	0003254	biological_process	regulation of membrane depolarization
J	0005198	molecular_function	structural molecule activity
J	0005515	molecular_function	protein binding
J	0005576	cellular_component	extracellular region
J	0005615	cellular_component	extracellular space
J	0005765	cellular_component	lysosomal membrane
J	0005794	cellular_component	Golgi apparatus
J	0005829	cellular_component	cytosol
J	0005886	cellular_component	plasma membrane
J	0006826	biological_process	iron ion transport
J	0006879	biological_process	intracellular iron ion homeostasis
J	0006955	biological_process	immune response
J	0006968	biological_process	cellular defense response
J	0007608	biological_process	sensory perception of smell
J	0007611	biological_process	learning or memory
J	0009897	cellular_component	external side of plasma membrane
J	0010038	biological_process	response to metal ion
J	0010977	biological_process	negative regulation of neuron projection development
J	0019731	biological_process	antibacterial humoral response
J	0019885	biological_process	antigen processing and presentation of endogenous peptide antigen via MHC class I
J	0019886	biological_process	antigen processing and presentation of exogenous peptide antigen via MHC class II
J	0023026	molecular_function	MHC class II protein complex binding
J	0030670	cellular_component	phagocytic vesicle membrane
J	0031902	cellular_component	late endosome membrane
J	0033077	biological_process	T cell differentiation in thymus
J	0033572	biological_process	transferrin transport
J	0034756	biological_process	regulation of iron ion transport
J	0034757	biological_process	negative regulation of iron ion transport
J	0042026	biological_process	protein refolding
J	0042605	molecular_function	peptide antigen binding
J	0042612	cellular_component	MHC class I protein complex
J	0042613	cellular_component	MHC class II protein complex
J	0042802	molecular_function	identical protein binding
J	0042803	molecular_function	protein homodimerization activity
J	0042824	cellular_component	MHC class I peptide loading complex
J	0045087	biological_process	innate immune response
J	0045646	biological_process	regulation of erythrocyte differentiation
J	0048260	biological_process	positive regulation of receptor-mediated endocytosis
J	0048261	biological_process	negative regulation of receptor-mediated endocytosis
J	0050680	biological_process	negative regulation of epithelial cell proliferation
J	0050768	biological_process	negative regulation of neurogenesis
J	0050778	biological_process	positive regulation of immune response
J	0050829	biological_process	defense response to Gram-negative bacterium
J	0050830	biological_process	defense response to Gram-positive bacterium
J	0050870	biological_process	positive regulation of T cell activation
J	0051289	biological_process	protein homotetramerization
J	0060586	biological_process	multicellular organismal-level iron ion homeostasis
J	0061844	biological_process	antimicrobial humoral immune response mediated by antimicrobial peptide
J	0071222	biological_process	cellular response to lipopolysaccharide
J	0071281	biological_process	cellular response to iron ion
J	0071283	biological_process	cellular response to iron(III) ion
J	0071316	biological_process	cellular response to nicotine
J	1990000	biological_process	amyloid fibril formation
J	1990712	cellular_component	HFE-transferrin receptor complex
J	2000774	biological_process	positive regulation of cellular senescence
J	2000978	biological_process	negative regulation of forebrain neuron differentiation

Functional Information from PDB Data

site_id	AC1
Number of Residues	8
Details	binding site for residue EDO A 301

Chain	Residue
A	HIS188
A	TRP204
A	LEU206
A	GLN242
A	HOH403
B	SER11
B	PRO14
B	HOH210

---

site_id	AC2
Number of Residues	8
Details	binding site for residue EDO B 101

Chain	Residue
B	ASN42
B	GLY43
B	THR77
B	ALA79
B	TYR94
F	PRO195
F	GLU196
B	LEU40

---

site_id	AC3
Number of Residues	7
Details	binding site for residue EDO B 102

Chain	Residue
B	ASP76
B	THR77
B	TYR78
B	TRP95
B	ARG97
B	HOH220
F	ARG193

---

site_id	AC4
Number of Residues	2
Details	binding site for residue EDO D 101

Chain	Residue
C	CYS121
D	ILE1

---

site_id	AC5
Number of Residues	4
Details	binding site for residue EDO F 302

Chain	Residue
F	LYS146
F	HOH402
H	TYR8
P	TYR8

---

site_id	AC6
Number of Residues	5
Details	binding site for residue EDO F 303

Chain	Residue
A	VAL76
A	THR80
A	ARG83
F	LYS146
F	GLN149

---

site_id	AC7
Number of Residues	5
Details	binding site for residue GOL F 304

Chain	Residue
F	ALA236
F	GLY237
F	ASP238
G	ARG12
G	ILE22

---

site_id	AC8
Number of Residues	4
Details	binding site for residue EDO I 301

Chain	Residue
E	TYR8
I	LYS146
I	HOH401
K	TYR8

---

site_id	AC9
Number of Residues	9
Details	binding site for Di-peptide GOL F 301 and CYS F 121

Chain	Residue
F	ALA117
F	TYR118
F	ASP119
F	GLY120
F	ASP122
F	TYR123
I	ASN86
I	GLN87
I	SER88

---

Functional Information from PROSITE/UniProt

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

Chain	Residue	Details
B	TYR78-HIS84
A	TYR257-HIS263

---

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	620
Details	Domain: {"description":"Ig-like C1-type"}

Chain

Residue

Details

---

site_id	SWS_FT_FI2
Number of Residues	273
Details	Region: {"description":"Alpha-2"}

Chain

Residue

Details

---

site_id	SWS_FT_FI3
Number of Residues	273
Details	Region: {"description":"Alpha-3"}

Chain

Residue

Details

---

site_id	SWS_FT_FI4
Number of Residues	8
Details	Glycosylation: {"description":"N-linked (GlcNAc...) asparagine","evidences":[{"evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

---