2A6K - JenaLib

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Biological Unit 3 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE ANALYSIS OF THE GERMLINE ANTIBODY 36-65 FAB IN COMPLEX WITH THE DODECAPEPTIDE SLGDNLTNHNLR

Authors :   D. K. Sethi, A. Agarwal, V. Manivel, K. V. Rao, D. M. Salunke

Date :   03 Jul 05 (Deposition) - 13 Jun 06 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.00

Chains :   Asym. Unit : A,B,H,L,P
Biol. Unit 1: A,B  (1x)
Biol. Unit 2: H,L,P  (1x)
Biol. Unit 3: H,L  (1x)

Keywords :   Immunoglobulin Fold, Fab-Peptide Complex, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. K. Sethi, A. Agarwal, V. Manivel, K. V. Rao, D. M. Salunke
Differential Epitope Positioning Within The Germline Antibody Paratope Enhances Promiscuity In The Primary Immune Response.
Immunity V. 24 429 2006
PubMed-ID: 16618592 | Reference-DOI: 10.1016/J.IMMUNI.2006.02.010
(for further references see the PDB file header)

Molecule 1 - GERMLINE ANTIBODY 36-65 FAB LIGHT CHAIN
	Chains	:	A, L
	Fragment	:	FAB
	Organism Common	:	HOUSE MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Other Details	:	MOUSE MONOCLONAL

Molecule 2 - GERMLINE ANTIBODY 36-65 FAB HEAVY CHAIN
	Chains	:	B, H
	Fragment	:	FAB
	Organism Common	:	HOUSE MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Other Details	:	MOUSE MONOCLONAL

Molecule 3
	Chains	:	P
	Engineered	:	YES
	Other Details	:	SYNTHESIZED PEPTIDE
	Synthetic	:	YES

		1	2	3	4	5
Asymmetric Unit	:	A	B	H	L	P
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:			H	L	P
Biological Unit 3 (1x)	:			H	L

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 2A6K)

(no "Site" information available for 2A6K)

Asymmetric Unit

No.	Residues
1	A:23	-	A:88
2	A:134	-	A:194
3	B:22	-	B:96
4	B:148	-	B:203
5	H:22	-	H:96
6	H:148	-	H:203
7	L:23	-	L:88
8	L:134	-	L:194

Asymmetric Unit

No.	Residues
1	Leu A:94	-	Pro A:95
2	Tyr A:140	-	Pro A:141
3	Phe B:154	-	Pro B:155
4	Glu B:156	-	Pro B:157
5	Arg B:196	-	Pro B:197
6	Leu L:94	-	Pro L:95
7	Tyr L:140	-	Pro L:141
8	Phe H:154	-	Pro H:155
9	Glu H:156	-	Pro H:157
10	Arg H:196	-	Pro H:197

(no "SAP(SNP)/Variant" information available for 2A6K)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	IG_MHC	PS00290	Immunoglobulins and major histocompatibility complex proteins signature.	IGKC_MOUSE	84-90	2	A:192-198 L:192-198

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	IG_MHC	PS00290	Immunoglobulins and major histocompatibility complex proteins signature.	IGKC_MOUSE	84-90	1	A:192-198 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	IG_MHC	PS00290	Immunoglobulins and major histocompatibility complex proteins signature.	IGKC_MOUSE	84-90	1	- L:192-198

Biological Unit 3 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	IG_MHC	PS00290	Immunoglobulins and major histocompatibility complex proteins signature.	IGKC_MOUSE	84-90	1	- L:192-198

(no "Exon" information available for 2A6K)

Asymmetric 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: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 ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2a6kA01 A:1-107 Immunoglobulins                                                                            2a6kA02 A:108-211 Immunoglobulins                                                                       --- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee....eeee......eeeeee.......eeeeee.....eeeee.............eeeeee..eeeeee...hhhhh.eeeeee......ee...eeeee.......eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee........eeeee.........eeeeeeeeeehhhhhh..eeeeeeee..eeeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------IG_MHC ---------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2a6k A   1 DIQMTQTTSSLSASLGDRVTISCRASQDISNYLNWYQQKPDGTVKLLIYYTSRLHSGVPSRFSGSGSGTDYSLTISNLEQEDIATYFCQQGNTLPRTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC 214
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210

Chain B from PDB  Type:PROTEIN  Length:218
 aligned with Q6PF95_MOUSE | Q6PF95 from UniProtKB/TrEMBL  Length:464

    Alignment length:222
                                                                                                                                   119                                                                                                                    
                                                                                                                                118  |                                                                                                                    
                                                                                                                          116  117|  |                                                                                                                    
                                    29        39        49        59        69        79        89        99       109      |  - ||  | 123       133       143       153       163       173       183       193       203       213       223       233  
         Q6PF95_MOUSE    20 QVQLKQSGAELVRPGASVKLSCKASGYIFTSYWIHWVKQRSGQGLEWIARIYPGTGSTYYNEKFKGKATLTADKSSSTAFMQLSSLKSEDSAVYFCA----YG--YDALYWGQGTPITVSSAKTTAPSVYPLAPVCGDTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPVVLQSDLYTLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIEPRG 235
               SCOP domains --------------------------------------------------------------------------------------------------------------d2a6kb1 B:111-219 Immunogl    obulin heavy chain gamma constant domain 1, CH1-gamma                          --- SCOP domains
               CATH domains 2a6kB01 B:1-121 Immunoglobulins                                                                                          2a6kB02 B:122-2    21 Immunoglobulins                                                               - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeee...ee.....eeeeeeeee..hhhhh.eeeeee.....eeeeeee......eee.......eeeeee....eeeeeee..hhhhheeeeeeeee......eeeee...eeee.........eeeee....----..eeeeeeeeeee.....eeee.hhh....eee...ee....eeeeeeeeee.........eeeeeehhhheeeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2a6k B   1 EVQLQQSGAELVRAGSSVKMSCKASGYTFTSYGINWVKQRPGQGLEWIGYINPGNGYTKYNEKFKGKTTLTVDKSSSTAYMQLRSLTSEDSAVYFCARSVYYGGSYYFDYWGQGTTLTVSSAKTTPPSVYPLAPGS----NSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSPRPSETVTCNVAHPASSTKVDKKIVPRD 222
                                    10        20        30        40        50        60        70        80        90       100       110       120       130     |   -|      150       160       170       180       190       200       210       220  
                                                                                                                                                                 136  141

Chain H from PDB  Type:PROTEIN  Length:216
 aligned with Q6PF95_MOUSE | Q6PF95 from UniProtKB/TrEMBL  Length:464

    Alignment length:222
                                                                                                                                   119                                                                                                                    
                                                                                                                                118  |                                                                                                                    
                                                                                                                          116  117|  |                                                                                                                    
                                    29        39        49        59        69        79        89        99       109      |  - ||  | 123       133       143       153       163       173       183       193       203       213       223       233  
         Q6PF95_MOUSE    20 QVQLKQSGAELVRPGASVKLSCKASGYIFTSYWIHWVKQRSGQGLEWIARIYPGTGSTYYNEKFKGKATLTADKSSSTAFMQLSSLKSEDSAVYFCA----YG--YDALYWGQGTPITVSSAKTTAPSVYPLAPVCGDTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPVVLQSDLYTLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIEPRG 235
               SCOP domains --------------------------------------------------------------------------------------------------------------d2a6kh1 H:111-219 Immunog      lobulin heavy chain gamma constant domain 1, CH1-gamma                        --- SCOP domains
               CATH domains 2a6kH01 H:1-121 Immunoglobulins                                                                                          2a6kH02 H:122-      221 Immunoglobulins                                                             - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eee....ee......eee..eee..hhhhh.eeeeee.....eeeeeee......eee.......eeeee......eeeee...hhhhheeeeeeeeee....eeeeee...eeee.........eeeee...------.eeeeeeeeeee.....eeee.hhh.....ee...ee....eeeeeeeeee.........eeeeeehhhheeeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2a6k H   1 EVQLQQSGAELVRAGSSVKMSCKASGYTFTSYGINWVKQRPGQGLEWIGYINPGNGYTKYNEKFKGKTTLTVDKSSSTAYMQLRSLTSEDSAVYFCARSVYYGGSYYFDYWGQGTTLTVSSAKTTPPSVYPLAPG------SMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSPRPSETVTCNVAHPASSTKVDKKIVPRD 222
                                    10        20        30        40        50        60        70        80        90       100       110       120       130    |    - |     150       160       170       180       190       200       210       220  
                                                                                                                                                                135    142

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 ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2a6kL01 L:1-107 Immunoglobulins                                                                            2a6kL02 L:108-211 Immunoglobulins                                                                       --- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeee......eeeee........eeeeee.....eeeee.............eeeeee..eeeeee...hhhhh.eeeeee......ee...eeeee.......eeeee..hhhhhh..eeeeeeeeeee.....eeeeee...ee...eeeee.........eeeeeeeeeehhhhh...eeeeeee.......eeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------IG_MHC ---------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2a6k L   1 DIQMTQTTSSLSASLGDRVTISCRASQDISNYLNWYQQKPDGTVKLLIYYTSRLHSGVPSRFSGSGSGTDYSLTISNLEQEDIATYFCQQGNTLPRTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC 214
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210

Chain P from PDB  Type:PROTEIN  Length:10
                                          
               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
                 2a6k P   3 GDNLTNHNLR  12
                                    12

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 '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: Immunoglobulin-like beta-sandwich (7299)

Superfamily: Immunoglobulin (5995)

Family: C1 set domains (antibody constant domain-like) (3013)

Protein domain: Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma (608)

Mouse (Mus musculus) [TaxId: 10090] (414)

1a	d2a6kb1	B:111-219
1b	d2a6kh1	H:111-219

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Sandwich (5577)

Topology: Immunoglobulin-like (3897)

Homologous Superfamily: Immunoglobulins (2282)

House mouse (Mus musculus) (616)

1a	2a6kA02	A:108-211
1b	2a6kB02	B:122-221
1c	2a6kH02	H:122-221
1d	2a6kL02	L:108-211
1e	2a6kB01	B:1-121
1f	2a6kH01	H:1-121
1g	2a6kA01	A:1-107
1h	2a6kL01	L:1-107

(no "Pfam Domain" information available for 2A6K)

Asymmetric Unit(hide GO term definitions)

Chain A,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.

Chain B,H (Q6PF95_MOUSE | Q6PF95)

Asymmetric Unit
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	Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 2a6k)

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(no "Sites" information available for 2a6k)

	Cis Peptide Bonds
		Arg B:196 - Pro B:197	[ RasMol ]
		Arg H:196 - Pro H:197	[ RasMol ]
		Glu B:156 - Pro B:157	[ RasMol ]
		Glu H:156 - Pro H:157	[ RasMol ]
		Leu A:94 - Pro A:95	[ RasMol ]
		Leu L:94 - Pro L:95	[ RasMol ]
		Phe B:154 - Pro B:155	[ RasMol ]
		Phe H:154 - Pro H:155	[ RasMol ]
		Tyr A:140 - Pro A:141	[ RasMol ]
		Tyr L:140 - Pro L:141	[ RasMol ]

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		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]
		Biological Unit 3	[ Jena3D ]

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Description

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