1KB5 - JenaLib

Molecule 1 - KB5-C20 T-CELL ANTIGEN RECEPTOR
	Cell	:	T-CELL
	Cellular Location	:	SURFACE
	Chains	:	A
	Engineered	:	YES
	Expression System	:	MUS MUSCULUS
	Expression System Cellular Location	:	MYELOMA
	Expression System Common	:	HOUSE MOUSE
	Expression System Taxid	:	10090
	Fragment	:	FV FRAGMENT, VARIABLE DOMAIN
	Organism Common	:	HOUSE MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Other Details	:	24 RESIDUE LINK BETWEEN VALPHA C-TERMINUS AND VBETA N-TERMINUS
	Synonym	:	TCR VAPLHA VBETA DOMAIN

Molecule 2 - KB5-C20 T-CELL ANTIGEN RECEPTOR
	Cell	:	T-CELL
	Cellular Location	:	SURFACE
	Chains	:	B
	Engineered	:	YES
	Expression System	:	MUS MUSCULUS
	Expression System Cellular Location	:	MYELOMA
	Expression System Common	:	HOUSE MOUSE
	Expression System Taxid	:	10090
	Fragment	:	FV FRAGMENT, VARIABLE DOMAIN
	Organism Common	:	HOUSE MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Other Details	:	24 RESIDUE LINK BETWEEN VALPHA C-TERMINUS AND VBETA N-TERMINUS
	Synonym	:	TCR VAPLHA VBETA DOMAIN

Molecule 3 - ANTIBODY DESIRE-1
	Chains	:	L
	Fragment	:	FAB
	Organism Common	:	HOUSE MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Other Details	:	CLEAVED BY PAPAIN
	Strain	:	IGG2A

Molecule 4 - ANTIBODY DESIRE-1
	Chains	:	H
	Fragment	:	FAB
	Organism Common	:	HOUSE MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Other Details	:	CLEAVED BY PAPAIN
	Strain	:	IGG2A

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (7, 7)

Cis Peptide Bonds (7, 7)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 1)

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:115
                                                                                                                                                    
               SCOP domains d1kb5a_ A: T-cell antigen receptor                                                                                  SCOP domains
               CATH domains 1kb5A00 A:1-120 Immunoglobulins                                                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee..eeee.....eeeeeee.........eeee......eeee.......eeee..eeeeeehhh.eeeeee....hhh.eeee................eeeee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------- Transcript
                1kb5 A    1 QQVRQSPQSLTVWEGETAILNCSYEDSTFNYFPWYQQFPGEGPALLISIRSVSDKKEDGRFTIFFNKREKKLSLHITDSQPGDSATYFCAARYQGGRALIFGTGTTVSVSPGSAD  120
                                    10        20        30        40        50        61        71        81        91     ||105       115     
                                                                                     59|                                  97||                 
                                                                                      61                                  101|                 
                                                                                                                           103

Chain B from PDB  Type:PROTEIN  Length:117
 aligned with TVB6_MOUSE | P04214 from UniProtKB/Swiss-Prot  Length:136

    Alignment length:117
                                                                                                                             119                 
                                                                                                                          118  |                 
                                    31        41        51        61        71        81        91       101       111      |119       129       
          TVB6_MOUSE     22 VTLLEQNPRWRLVPRGQAVNLRCILKNSQYPWMSWYQQDLQKQLQWLFTLRSPRDKEVKSLPGADYLATRVTDTELRLQVANMSQGRTLYCTCSATG--GLNTGQLYFGEGSKLTVL  136
               SCOP domains d1kb5b_ B: T-cell antigen receptor                                                                                    SCOP domains
               CATH domains 1kb5B00 B:1-116A Immunoglobulins                                                                                      CATH domains
               Pfam domains -V-set-1kb5B01 B:2-116                                                                                              - Pfam domains
         Sec.struct. author ...eeee............eeeeee......eeeeeee.....eeeeeee....eeeeeee..eeeeeee....eeeeeee.....eeeeeeee...........eee...eee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------- Transcript
                1kb5 B    1 VTLLEQNPRWRLVPRGQAVNLRCILKNSQYPWMSWYQQDLQKQLQWLFTLRSPGDKEVKSLPGADYLATRVTDTELRLQVANMSQGRTLYCTCSAAPDWGASAETLYFGSGTRLTVL 116A
                                    10        20        30|       39        49        59        69        79       |91       101    |  110      |
                                                        30A                                                       87|            105A        116A
                                                                                                                   90

Chain H from PDB  Type:PROTEIN  Length:219
                                                                                                                                                                                                                                                            
               SCOP domains d1kb5h1 H:1-113 Immunoglobulin heavy chain variable domain, VH                                                         d1kb5h2 H:114-213 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                      SCOP domains
               CATH domains 1kb5H01 H:1-113 Immunoglobulins                                                                                        1kb5H02 H:114-212 Immunoglobulins                                                                  - CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee.......eeeeeeehhh..eeeeeeee.....eee.......eeeeee....eeeeee..........eeeeee...............eee........eeeee...........eeeeeeeeee.....eeee........eeee..eee..eeeeeeeeee..........eeeeeehhh.eeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1kb5 H    1 EVQLQQSGPELEKPGASVKISCKASGYSFTGYNMNWVKQSNGKSLEWIGNIDPYYGGISYNQKFKGRATLTVDKSSSTAYMQLKSLTSEDSAVYYCARSRTDLYYFDYWGQGTTLTVSSAKTTAPSVYPLAPVCGDTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIEPR  213
                                    10        20        30        40        50  |     59        69        79   |||  86        96    || 104       114       124       134       144       154       164       174       184       194       204         
                                                                              52A                            82A||               100J|                                                                                                                 
                                                                                                              82B|                100K                                                                                                                 
                                                                                                               82C

Chain L from PDB  Type:PROTEIN  Length:214
 aligned with IGKC_MOUSE | P01837 from UniProtKB/Swiss-Prot  Length:106

    Alignment length:214
                                                                                                                                        1                                                                                                         
                                     -         -         -         -         -         -         -         -         -         -        |2        12        22        32        42        52        62        72        82        92       102    
          IGKC_MOUSE      - ------------------------------------------------------------------------------------------------------------ADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC  106
               SCOP domains d1kb5l1 L:1-108 Immunoglobulin light chain kappa variable domain, VL-kappa                                  d1kb5l2 L:109-214 Immunoglobulin light chain kappa constant domain, CL-kappa                               SCOP domains
               CATH domains 1kb5L01 L:1-108 Immunoglobulins                                                                             1kb5L02 L:109-214 Immunoglobulins                                                                          CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------C1-set-1kb5L01 L:119-206                                                                -------- Pfam domains
         Sec.struct. author ....eee..eee......eeeeee........eeeeee......eeee.............eeeeee..eeeeee....hhh.eeeeeee...........eeee........eeeee...hhhhhh..eeeeeeee.......eeeeee........eeeee...........eeeeeee.hhhhh...eeeeeee.......eeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------IG_MHC ---------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1kb5 L    1 DIQMTQSPASLSASVGETVTITCRASKNIYSYLAWYQQKQGKSPQLLVYNAKTLGEGVPSRFSGSGSGTQFSLKINSLQPEDFGSYYCQHHYGTPYTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC  214
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210

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 (6, 6)

CATH Domains (1, 6)

Pfam Domains (2, 2)

Gene Ontology (30, 43)

Asymmetric/Biological Unit(hide GO term definitions)

Chain B (TVB6_MOUSE | P04214)

Chain L (IGKC_MOUSE | P01837)

molecular function
	GO:0003823	antigen binding	Interacting selectively and non-covalently with an antigen, any substance which is capable of inducing a specific immune response and of reacting with the products of that response, the specific antibody or specifically sensitized T-lymphocytes, or both. Binding may counteract the biological activity of the antigen.
	GO:0034987	immunoglobulin receptor binding	Interacting selectively and non-covalently with one or more specific sites on an immunoglobulin receptor molecule.
biological process
	GO:0030183	B cell differentiation	The process in which a precursor cell type acquires the specialized features of a B cell. A B cell is a lymphocyte of B lineage with the phenotype CD19-positive and capable of B cell mediated immunity.
	GO:0050853	B cell receptor signaling pathway	A series of molecular signals initiated by the cross-linking of an antigen receptor on a B cell.
	GO:0006958	complement activation, classical pathway	Any process involved in the activation of any of the steps of the classical pathway of the complement cascade which allows for the direct killing of microbes, the disposal of immune complexes, and the regulation of other immune processes.
	GO:0042742	defense response to bacterium	Reactions triggered in response to the presence of a bacterium that act to protect the cell or organism.
	GO:0045087	innate immune response	Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
	GO:0006911	phagocytosis, engulfment	The internalization of bacteria, immune complexes and other particulate matter or of an apoptotic cell by phagocytosis, including the membrane and cytoskeletal processes required, which involves one of three mechanisms: zippering of pseudopods around a target via repeated receptor-ligand interactions, sinking of the target directly into plasma membrane of the phagocytosing cell, or induced uptake via an enhanced membrane ruffling of the phagocytosing cell similar to macropinocytosis.
	GO:0006910	phagocytosis, recognition	The initial step in phagocytosis involving adhesion to bacteria, immune complexes and other particulate matter, or an apoptotic cell and based on recognition of factors such as bacterial cell wall components, opsonins like complement and antibody or protein receptors and lipids like phosphatidyl serine, and leading to intracellular signaling in the phagocytosing cell.
	GO:0050871	positive regulation of B cell activation	Any process that activates or increases the frequency, rate or extent of B cell activation.
cellular component
	GO:0072562	blood microparticle	A phospholipid microvesicle that is derived from any of several cell types, such as platelets, blood cells, endothelial cells, or others, and contains membrane receptors as well as other proteins characteristic of the parental cell. Microparticles are heterogeneous in size, and are characterized as microvesicles free of nucleic acids.
	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:0042571	immunoglobulin complex, circulating	An immunoglobulin complex that is secreted into extracellular space and found in mucosal areas or other tissues or circulating in the blood or lymph. In its canonical form, a circulating immunoglobulin complex is composed of two identical heavy chains and two identical light chains, held together by disulfide bonds. Some forms of are polymers of the basic structure and contain additional components such as J-chain and the secretory component.
	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.

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Access by PDB/NDB ID
	1kb5
		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
	GCAM_MOUSE \| P01865
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt
	IGKC_MOUSE \| P01837
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt
	TVB6_MOUSE \| P04214
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	(no 'Enzyme Classificator' available)
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Description

Compounds