2PXY - JenaLib

Molecule 1 - T CELL RECEPTOR ALPHA CHAIN
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PAK400
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Common	:	HOUSE MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090

Molecule 2 - T CELL RECEPTOR BETA CHAIN
	Chains	:	B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PAK400
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Mutation	:	YES
	Organism Common	:	HOUSE MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090

Molecule 3 - H-2 CLASS II HISTOCOMPATIBILITY ANTIGEN, A-U ALPHA CHAIN
	Chains	:	C
	Engineered	:	YES
	Expression System	:	DROSOPHILA MELANOGASTER
	Expression System Common	:	FRUIT FLY
	Expression System Taxid	:	7227
	Fragment	:	EXTRACELLULAR ALPHA-1, EXTRACELLULAR ALPHA-2
	Organism Common	:	HOUSE MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090

Molecule 4 - H-2 CLASS II HISTOCOMPATIBILITY ANTIGEN, A-U BETA CHAIN
	Chains	:	D
	Engineered	:	YES
	Expression System	:	DROSOPHILA MELANOGASTER
	Expression System Common	:	FRUIT FLY
	Expression System Taxid	:	7227
	Fragment	:	EXTRACELLULAR BETA-1, EXTRACELLULAR BETA-2
	Organism Common	:	HOUSE MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090

Molecule 5 - MYELIN BASIC PROTEIN (MBP)-PEPTIDE
	Chains	:	P
	Engineered	:	YES
	Mutation	:	YES
	Other Details	:	SYNTHETIC CONSTRUCT. THE SEQUENCE CAN BE NATURALLY FOUND IN MUS MUSCULUS (MOUSE)
	Synthetic	:	YES

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (5, 5)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (0, 0)

Sequences/Alignments

Asymmetric/Biological Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:114
 aligned with Q5R1F5_MOUSE | Q5R1F5 from UniProtKB/TrEMBL  Length:112

    Alignment length:114
                                                                                                                       112                    
                                    28        38        48        58        68        78        88        98       108   |     -         -    
        Q5R1F5_MOUSE     19 QGDSVTQTEGQVALSEEDFLTIHCNYSASGYPALFWYVQYPGEGPQFLFRASRDKEKGSSRGFEATYNKEATSFHLQKASVQESDSAVYYCALS--------------------    -
               SCOP domains d2pxya_ A: automated matches                                                                                       SCOP domains
               CATH domains 2pxyA00 A:-1-116 Immunoglobulins                                                                                   CATH domains
               Pfam domains --V-set-2pxyA01 A:1-93                                                                        -------------------- Pfam domains
         Sec.struct. author ...eeee...eeeee....eee.eeee.....eeeeeee......eeeeee.....eeee..eeee.........eee...hhhhheeeeeeee........ee...eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------ Transcript
                2pxy A   -1 SADSVTQTGGQVALSEEDFLTIHCNYSASGYPALFWYVQYPGEGPQFLFRASRDKEKGSSRGFEATYNKEATSFHLQKASVQESDSAVYYCALSENYGNEKITFGAGTKLQVVP  116
                                     8        18        28        38        48        58||      69        79        89   ||  102       112    
                                                                                       59|                              93|   |               
                                                                                        61                               98   |               
                                                                                                                           101A

Chain B from PDB  Type:PROTEIN  Length:111
 aligned with A2NTY6_MOUSE | A2NTY6 from UniProtKB/TrEMBL  Length:144

    Alignment length:113
                                    41        51        61        71        81        91       101       111       121       131       141   
        A2NTY6_MOUSE     32 AVTQSPRNKVAVTGGKVTLSCNQTNNHNNMYWYRQDTGHGLRLIHYSYGAGSTEKGDIPDGYKASRPSQENFSLILELATPSQTSVYFCASGELGGFNQDTQYFGPGTRLLVL  144
               SCOP domains d2pxyb_ B: automated matches                                                                                      SCOP domains
               CATH domains 2pxyB00 B:3-117 Immunoglobulins                                                                                   CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee..eeee.....eeeeeee.....eeeeeeee...eeeeeeee......ee.......eee.......eeee...hhhhheeeeeeee.....--...ee...eeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------- Transcript
                2pxy B    3 AVTQSPRNKVAVTGEKVTLSCNQTNNHNNMYWYRQDTGHGLRLIYYSYGAGSTEKGDIPDGYKASRPSQENFSLTLESATPSQTSVYFCASGDASGA--ETLYFGPGTRLTVL  117
                                    12        22        32        42        52        62||      73        83        93      |104       114   
                                                                                       63|                                100  |             
                                                                                        65                                   104

Chain C from PDB  Type:PROTEIN  Length:183
 aligned with HA2U_MOUSE | P14438 from UniProtKB/Swiss-Prot  Length:227

    Alignment length:183
                                 1                                                                                                                                                                                 
                                 |   5        15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175   
          HA2U_MOUSE      - -----DHVGSYGIVVYQSPGDIGQYTFEFDGDELFYVDLDKKETIWMLPEFAQLRSFDPQGGLQNIATGKHNLGVLTKRSNSTPATNEAPQATVFPKSPVLLGQPNTLICFVDNIFPPVINITWLRNSKSVADGVYETSFFVNRDYSFHKLSYLTFIPSDDDIYDCKVEHWGLEEPVLKHWEP  178
               SCOP domains --d2pxyc2 C:1-81 Class II MHC alpha chain, N-terminal domain                        d2pxyc1 C:82-180 Class II MHC alpha chain, C-terminal domain                                        SCOP domains
               CATH domains ----2pxyC01 C:3-81                                                                  2pxyC02 C:82-180 Immunoglobulins                                                                    CATH domains
               Pfam domains -----MHC_II_alpha-2pxyC02 C:4-84                                                       --------C1-set-2pxyC01 C:93-175                                                            ----- Pfam domains
         Sec.struct. author ......eeeeeeeeeeee...eeeeeeee..eeeeeee....eeee.hhhhhh....hhhhhhhhhhhhhhhhhhhhhhh..........eeeeee.........eeeeeeeeee.....eeeeee..ee....eee...ee.....eeeeeeeee.......eeeeee.......eeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------IG_MHC ------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2pxy C   -1 DDIEADHVGSYGIVVYQSPGDIGQYTFEFDGDELFYVDLDKKETIWMLPEFAQLRSFDPQGGLQNIATGKHNLGVLTKRSNSTPATNEAPQATVFPKSPVLLGQPNTLICFVDNIFPPVINITWLRNSKSVADGVYETSFFVNRDYSFHKLSYLTFIPSDDDIYDCKVEHWGLEEPVLKHWEP  180
                                     8 |      17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177   
                                      9A

Chain D from PDB  Type:PROTEIN  Length:189
 aligned with HB2U_MOUSE | P06344 from UniProtKB/Swiss-Prot  Length:263

    Alignment length:189
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208         
          HB2U_MOUSE     29 DSERHFVVQFQPFCYFTNGTQRIRYVTRYIYNREEYLRFDSDVGEYRAVTELGRPDAEYYNKQYLERTRAELDTVCRYNYEETEVPTSLRRLEQPNVVISLSRTEALNHHNTLVCSVTDFYPAKIKVRWFRNGQEETVGVSSTQLIRNGDWTFQVLVMLEMTPRRGEVYTCHVEHPSLKSPITVEWRAQ  217
               SCOP domains --d2pxyd2 D:4-93 Class II MHC beta chain, N-terminal domain                                d2pxyd1 D:94-191 Class II MHC beta chain, C-terminal domain                                        SCOP domains
               CATH domains 2pxyD01 D:2-92 Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1       2pxyD02 D:93-191 Immunoglobulins                                                                    CATH domains
               Pfam domains ------------MHC_II_beta-2pxyD02 D:14-86                                             ----------------C1-set-2pxyD01 D:103-191                                                                  Pfam domains
         Sec.struct. author .....eeeeeeeeeeee....eeeeeeeeee..eeeeeee.....eee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhh....eeeeee.........eeeeeeeeee.....eeeeee..eee...eee...ee.....eeeeeeeee......eeeeeee.......eeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------IG_MHC -------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2pxy D    2 DSERHFVVQFQPFCYFTNGTQRIRYVTRYIYNREEYLRFDSDVGEYRAVTELGRPDAEYYNKQYLERTRAELDTVCRYNYEETEVPTSLRRLEQPNVVISLSRTEALNHHNTLVCSVTDFYPAKIKVRWFRNGQEETVGVSSTQLIRNGDWTFQVLVMLEMTPRRGEVYTCHVEHPSLKSPITVEWRAQ  191
                                    11        21        31        41        51        61  ||    73        83 |      92       102       112       122       132       142       152       162       172       182         
                                                                                         64|               84A                                                                                                           
                                                                                          67

Chain P from PDB  Type:PROTEIN  Length:11
                                            
               SCOP domains ----------- SCOP domains
               CATH domains ----------- CATH domains
               Pfam domains ----------- Pfam domains
         Sec.struct. author ........... Sec.struct. author
                 SAPs(SNPs) ----------- SAPs(SNPs)
                    PROSITE ----------- PROSITE
                 Transcript ----------- Transcript
                2pxy P   -2 RGGASQYRPSQ    8
                                     7

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Classification and Annotation

SCOP Domains (5, 6)

CATH Domains (2, 6)

Pfam Domains (4, 5)

Gene Ontology (15, 22)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (Q5R1F5_MOUSE | Q5R1F5)

Chain B (A2NTY6_MOUSE | A2NTY6)

Chain C (HA2U_MOUSE | P14438)

molecular function
	GO:0042605	peptide antigen binding	Interacting selectively and non-covalently with an antigen peptide.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
	GO:0019882	antigen processing and presentation	The process in which an antigen-presenting cell expresses antigen (peptide or lipid) on its cell surface in association with an MHC protein complex.
	GO:0019886	antigen processing and presentation of exogenous peptide antigen via MHC class II	The process in which an antigen-presenting cell expresses a peptide antigen of exogenous origin on its cell surface in association with an MHC class II protein complex. The peptide antigen is typically, but not always, processed from a whole protein.
	GO:0048002	antigen processing and presentation of peptide antigen	The process in which an antigen-presenting cell expresses peptide antigen in association with an MHC protein complex on its cell surface, including proteolysis and transport steps for the peptide antigen both prior to and following assembly with the MHC protein complex. The peptide antigen is typically, but not always, processed from an endogenous or exogenous protein.
	GO:0002504	antigen processing and presentation of peptide or polysaccharide antigen via MHC class II	The process in which an antigen-presenting cell expresses antigen (peptide or polysaccharide) on its cell surface in association with an MHC class II protein complex.
	GO:0006955	immune response	Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat.
	GO:0002376	immune system process	Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats.
	GO:0045582	positive regulation of T cell differentiation	Any process that activates or increases the frequency, rate or extent of T cell differentiation.
cellular component
	GO:0042613	MHC class II protein complex	A transmembrane protein complex composed of an MHC class II alpha and MHC class II beta chain, and with or without a bound peptide or polysaccharide antigen.
	GO:0009897	external side of plasma membrane	The leaflet of the plasma membrane that faces away from the cytoplasm and any proteins embedded or anchored in it or attached to its surface.
	GO:0016021	integral component of membrane	The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0005764	lysosome	A small lytic vacuole that has cell cycle-independent morphology and is found in most animal cells and that contains a variety of hydrolases, most of which have their maximal activities in the pH range 5-6. The contained enzymes display latency if properly isolated. About 40 different lysosomal hydrolases are known and lysosomes have a great variety of morphologies and functions.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

Chain D (HB2U_MOUSE | P06344)

biological process
	GO:0019882	antigen processing and presentation	The process in which an antigen-presenting cell expresses antigen (peptide or lipid) on its cell surface in association with an MHC protein complex.
	GO:0002504	antigen processing and presentation of peptide or polysaccharide antigen via MHC class II	The process in which an antigen-presenting cell expresses antigen (peptide or polysaccharide) on its cell surface in association with an MHC class II protein complex.
	GO:0006955	immune response	Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat.
	GO:0002376	immune system process	Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats.
cellular component
	GO:0042613	MHC class II protein complex	A transmembrane protein complex composed of an MHC class II alpha and MHC class II beta chain, and with or without a bound peptide or polysaccharide antigen.
	GO:0016021	integral component of membrane	The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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	2pxy
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	A2NTY6_MOUSE \| A2NTY6
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/TrEMBL
	HA2U_MOUSE \| P14438
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt
	HB2U_MOUSE \| P06344
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt
	Q5R1F5_MOUSE \| Q5R1F5
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/TrEMBL

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Description

Compounds