2A6J - JenaLib

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Title :   CRYSTAL STRUCTURE ANALYSIS OF THE ANTI-ARSONATE GERMLINE ANTIBODY 36-65

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

Date :   02 Jul 05 (Deposition) - 13 Jun 06 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.70

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

Keywords :   Germline, Immunoglobulin Fold, 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 Immun Response.
Immunity V. 24 429 2006
PubMed-ID: 16618592 | Reference-DOI: 10.1016/J.IMMUNI.2006.02.010

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

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

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 2A6J)

(no "Site" information available for 2A6J)

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 L:94	-	Pro L:95
2	Tyr L:140	-	Pro L:141
3	Phe H:154	-	Pro H:155
4	Glu H:156	-	Pro H:157
5	Arg H:196	-	Pro H:197
6	Leu A:94	-	Pro A:95
7	Tyr A:140	-	Pro A:141
8	Phe B:154	-	Pro B:155
9	Glu B:156	-	Pro B:157
10	Arg B:196	-	Pro B:197

(no "SAP(SNP)/Variant" information available for 2A6J)

(no "PROSITE Motif" information available for 2A6J)

(no "Exon" information available for 2A6J)

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
                                                                                                                                                                                                                                                      
               SCOP domains d2a6ja1 A:1-107 automated matches                                                                          d2a6ja2 A:108-214 automated matches                                                                         SCOP domains
               CATH domains 2a6jA01 A:1-107 Immunoglobulins                                                                            2a6jA02 A:108-211 Immunoglobulins                                                                       --- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee....eee......eeeeeee.......eeeeee.....eeeeee....ee......eeeeee..eeeeee...hhhhh.eeeeee......ee...eeee........eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee........eeeee.........eeeeeeeeeehhhhh...eeeeeee.......eeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2a6j 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:222
                                                                                                                                                                                                                                                              
               SCOP domains --------------------------------------------------------------------------------------------------------------d2a6jb1 B:111-219 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                              --- SCOP domains
               CATH domains 2a6jB01 B:1-121 Immunoglobulins                                                                                          2a6jB02 B:122-221 Immunoglobulins                                                                   - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeee..ee.....eeeeeeee.......eeeeeee......eeeeee................eeeeee....eeeeee...hhhhheeeeeeeee......eeeee...eeeee........eeeee..........eeeeeeeeeee.....eeee.hhh....eee...ee....eeeeeeeeee.........eeeeeehhhheeeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2a6j B   1 EVQLQQSGAELVRAGSSVKMSCKASGYTFTSYGINWVKQRPGQGLEWIGYINPGNGYTKYNEKFKGKTTLTVDKSSSTAYMQLRSLTSEDSAVYFCARSVYYGGSYYFDYWGQGTTLTVSSAKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSPRPSETVTCNVAHPASSTKVDKKIVPRD 222
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220

Chain H from PDB  Type:PROTEIN  Length:222
                                                                                                                                                                                                                                                              
               SCOP domains --------------------------------------------------------------------------------------------------------------d2a6jh1 H:111-219 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                              --- SCOP domains
               CATH domains 2a6jH01 H:1-121 Immunoglobulins                                                                                          2a6jH02 H:122-221 Immunoglobulins                                                                   - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eee....eee.....eeeeeeee........eeeeee......eeeeee..................eeeehhh.eeeeee...hhhhheeeeeeeeeee..eeeeeee...eeeee........eeeee...........eeeeeeeeee.....eeee.hhh.....ee...ee....eeeeeeeee..hhhhhh..eeeeeehhhheeeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2a6j H   1 EVQLQQSGAELVRAGSSVKMSCKASGYTFTSYGINWVKQRPGQGLEWIGYINPGNGYTKYNEKFKGKTTLTVDKSSSTAYMQLRSLTSEDSAVYFCARSVYYGGSYYFDYWGQGTTLTVSSAKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSPRPSETVTCNVAHPASSTKVDKKIVPRD 222
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220

Chain L from PDB  Type:PROTEIN  Length:214
                                                                                                                                                                                                                                                      
               SCOP domains d2a6jl1 L:1-107 automated matches                                                                          d2a6jl2 L:108-214 automated matches                                                                         SCOP domains
               CATH domains 2a6jL01 L:1-107 Immunoglobulins                                                                            2a6jL02 L:108-211 Immunoglobulins                                                                       --- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee...eeee.....eeeeeee.......eeeeee.....eeeeeehhhhee......eeeeee..eeeeee...hhhhh.eeeeee......ee...eeeee.......eeeee..hhhhhh..eeeeeeeeeee.....eeeeee........eeeee.........eeeeeeeeeehhhhh...eeeeeee.........eeee.hhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2a6j 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

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: automated matches (864)

Protein domain: automated matches (864)

Mouse (Mus musculus) [TaxId: 10090] (360)

1a	d2a6ja1	A:1-107
1b	d2a6jl1	L:1-107

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

Protein domain: automated matches (652)

Mouse (Mus musculus) [TaxId: 10090] (309)

2a	d2a6ja2	A:108-214
2b	d2a6jl2	L:108-214

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

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

3a	d2a6jb1	B:111-219
3b	d2a6jh1	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	2a6jA02	A:108-211
1b	2a6jB02	B:122-221
1c	2a6jH02	H:122-221
1d	2a6jL02	L:108-211
1e	2a6jB01	B:1-121
1f	2a6jH01	H:1-121
1g	2a6jA01	A:1-107
1h	2a6jL01	L:1-107

(no "Pfam Domain" information available for 2A6J)

Asymmetric Unit(hide GO term definitions)

(no "Gene Ontology" information available for 2A6J)

Asymmetric Unit
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(no "Sites" information available for 2a6j)

	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 ]

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]
		Biological Unit 3	[ Jena3D ]

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2a6d	CRYSTAL STRUCTURE ANALYSIS OF THE ANTI-ARSONATE GERMLINE ANTIBODY 36-65 IN COMPLEX WITH A PHAGE DISPLAY DERIVED DODECAPEPTIDE RLLIADPPSPRE
2a6i	CRYSTAL STRUCTURE ANALYSIS OF THE ANTI-ARSONATE GERMLINE ANTIBODY 36-65 IN COMPLEX WITH A PHAGE DISPLAY DERIVED DODECAPEPTIDE KLASIPTHTSPL

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