1FL6 - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   THE HAPTEN COMPLEXED GERMLINE PRECURSOR TO SULFIDE OXIDASE CATALYTIC ANTIBODY 28B4

Authors :   J. Yin, E. C. Mundorff, P. L. Yang, K. U. Wendt, D. Hanway, R. C. Stevens, P. G. Schultz

Date :   11 Aug 00 (Deposition) - 14 Nov 01 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.80

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

Keywords :   Catalytic Antibody, Germline Antibody, Sulfide Oxidase, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. Yin, E. C. Mundorff, P. L. Yang, K. U. Wendt, D. Hanway, R. C. Stevens, P. G. Schultz
A Comparative Analysis Of The Immunological Evolution Of Antibody 28B4.
Biochemistry V. 40 10764 2001
PubMed-ID: 11535051 | Reference-DOI: 10.1021/BI010536C
(for further references see the PDB file header)

Molecule 1 - ANTIBODY GERMLINE PRECURSOR TO 28B4
	Chains	:	L, A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	LIGHT CHAIN (CHAINS L AND A)
	Mutation	:	YES
	Organism Common	:	HOUSE MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090

Molecule 2 - ANTIBODY GERMLINE PRECURSOR TO 28B4
	Chains	:	H, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	HEAVY CHAIN (CHAINS H AND B)
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 2)

No.	Name	Count	Type	Full Name
1	AAH	2	Ligand/Ion	1-[N-4'-NITROBENZYL-N-4'-CARBOXYBUTYLAMINO]METHYLPHOSPHONIC ACID

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	AAH	1	Ligand/Ion	1-[N-4'-NITROBENZYL-N-4'-CARBOXYBUTYLAMINO]METHYLPHOSPHONIC ACID

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	AAH	1	Ligand/Ion	1-[N-4'-NITROBENZYL-N-4'-CARBOXYBUTYLAMINO]METHYLPHOSPHONIC ACID

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TYR H:33 , ARG H:52 , ASP H:95 , GLY H:96 , ALA H:99 , GLU L:34 , GLY L:91 , VAL L:94 , ARG L:96 , HIS L:274	BINDING SITE FOR RESIDUE AAH H 824
2	AC2	SOFTWARE	TYR A:32 , GLU A:34 , SER A:92 , VAL A:94 , ARG A:96 , HIS A:274 , TYR B:33 , ARG B:52 , ASP B:95 , GLY B:96 , ALA B:99	BINDING SITE FOR RESIDUE AAH B 824

Asymmetric Unit

No.	Residues
1	A:23	-	A:88
2	A:134	-	A:194
3	B:22	-	B:92
4	B:140	-	B:196
5	H:22	-	H:92
6	H:140	-	H:196
7	L:23	-	L:88
8	L:134	-	L:194

Asymmetric Unit

No.	Residues
1	Thr L:7	-	Pro L:8
2	Val L:94	-	Pro L:95
3	Tyr L:140	-	Pro L:141
4	Phe H:146	-	Pro H:147
5	Glu H:148	-	Pro H:149
6	Thr A:7	-	Pro A:8
7	Val A:94	-	Pro A:95
8	Tyr A:140	-	Pro A:141
9	Phe B:146	-	Pro B:147
10	Glu B:148	-	Pro B:149

(no "SAP(SNP)/Variant" information available for 1FL6)

(no "PROSITE Motif" information available for 1FL6)

(no "Exon" information available for 1FL6)

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:217
                                                                                                                                                                                                                                                         
               SCOP domains d1fl6a1 A:1-107 Immunoglobulin light chain kappa variable domain, VL-kappa                                      d1fl6a2 A:108-212 Immunoglobulin light chain kappa constant domain, CL-kappa                              SCOP domains
               CATH domains --1fl6A01 A:3-108 Immunoglobulins                                                                                1fl6A02 A:109-211 Immunoglobulins                                                                      - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee..eeeee...eeeeeee.............eeeeee.....eeeee.............eeeeee..eeeeeee..hhhhheeeeeee......ee...eeeeee......eeeee..hhhhhhhheeeeeeeeeee.....eeeeee........eeeee.........eeeeeeeeeehhhhhh..eeeeeee.......eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1fl6 A   1 ELVMTQTPLSLPVSLGDQASISCRSSQSIVHSNGNTYLEWYLQKPGQSPKLLIYKVSNRFSGVPDRFSGSGSGTDFTLKISRVEAEDLGVYYCFQGSHVPRTFGGGTKLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRG 212
                                    10        20      |273 ||     35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       
                                                     27| 275|                                                                                                                                                                                        
                                                     271   28

Chain B from PDB  Type:PROTEIN  Length:219
                                                                                                                                                                                                                                                           
               SCOP domains d1fl6b1 B:1-113 Immunoglobulin heavy chain variable domain, VH                                                         d1fl6b2 B:114-213 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                      SCOP domains
               CATH domains 1fl6B01 B:1-113 Immunoglobulins                                                                                        1fl6B02 B:114-213 Immunoglobulins                                                                    CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..eee.....eeeeeeee..hhhhheeeeeee......eeeeee.hhhhh..eee.......eeeeee....eeeeee...hhhhheeeeeeeee..eeeee...eeeee........eeeee..........eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee........eeeeee......eeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1fl6 B   1 QVQLVESGGGLVQPGGSLRLSCATSGFTFTDYYMSWVRQPPGKALEWLGFIRNKANGYTTEYSASVKGRFTISRDNSQSILYLQMNTLRAEDSATYYCARDGSYAMDYWGQGTSVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEP 213
                                    10        20        30        40        50 || ||  57        67        77    || |84        94       104       114       124       134       144       154       164       174       184       194       204         
                                                                              52| ||                           82| ||                                                                                                                                  
                                                                              521 ||                           821 ||                                                                                                                                  
                                                                                523|                             823|                                                                                                                                  
                                                                                  53                               83

Chain H from PDB  Type:PROTEIN  Length:219
                                                                                                                                                                                                                                                           
               SCOP domains d1fl6h1 H:1-113 Immunoglobulin heavy chain variable domain, VH                                                         d1fl6h2 H:114-213 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                      SCOP domains
               CATH domains 1fl6H01 H:1-113 Immunoglobulins                                                                                        1fl6H02 H:114-213 Immunoglobulins                                                                    CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..eee.....eeeeeeee..hhhhheeeeeee......eeeeee.hhhhh..eee.......eeeeee....eeeeee...hhhhheeeeeeeee..eeeee...eeeee........eeeee..........eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee........eeeeee......eeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1fl6 H   1 QVQLVESGGGLVQPGGSLRLSCATSGFTFTDYYMSWVRQPPGKALEWLGFIRNKANGYTTEYSASVKGRFTISRDNSQSILYLQMNTLRAEDSATYYCARDGSYAMDYWGQGTSVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEP 213
                                    10        20        30        40        50 || ||  57        67        77    || |84        94       104       114       124       134       144       154       164       174       184       194       204         
                                                                              52| ||                           82| ||                                                                                                                                  
                                                                              521 ||                           821 ||                                                                                                                                  
                                                                                523|                             823|                                                                                                                                  
                                                                                  53                               83

Chain L from PDB  Type:PROTEIN  Length:217
                                                                                                                                                                                                                                                         
               SCOP domains d1fl6l1 L:1-107 Immunoglobulin light chain kappa variable domain, VL-kappa                                      d1fl6l2 L:108-212 Immunoglobulin light chain kappa constant domain, CL-kappa                              SCOP domains
               CATH domains --1fl6L01 L:3-108 Immunoglobulins                                                                                1fl6L02 L:109-211 Immunoglobulins                                                                      - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee....eee...eeeeeee.............eeeeee.....eeeee.............eeeeee..eeeeeee..hhhhh.eeeeee......ee......eee......eeeee..hhhhhhhheeeeeeeeeee.....eeeeee........eeeee.........eeeeeeeeeehhhhhh..eeeeeee.......eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1fl6 L   1 ELVMTQTPLSLPVSLGDQASISCRSSQSIVHSNGNTYLEWYLQKPGQSPKLLIYKVSNRFSGVPDRFSGSGSGTDFTLKISRVEAEDLGVYYCFQGSHVPRTFGGGTKLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRG 212
                                    10        20      |273 ||     35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       
                                                     27| 275|                                                                                                                                                                                        
                                                     271   28

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	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(

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Architectures( (-)

)

Topologies( (-)

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Homologous Superfamilies( (-)

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Organisms( (-)

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Class: Mainly Beta (13760)

Architecture: Sandwich (5577)

Topology: Immunoglobulin-like (3897)

Homologous Superfamily: Immunoglobulins (2282)

House mouse (Mus musculus) (616)

1a	1fl6A02	A:109-211
1b	1fl6A01	A:3-108
1c	1fl6L01	L:3-108
1d	1fl6B02	B:114-213
1e	1fl6H02	H:114-213
1f	1fl6B01	B:1-113
1g	1fl6H01	H:1-113
1h	1fl6L02	L:109-211

(no "Pfam Domain" information available for 1FL6)

Asymmetric Unit(hide GO term definitions)

(no "Gene Ontology" information available for 1FL6)

Asymmetric Unit
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	Cis Peptide Bonds
		Glu B:148 - Pro B:149	[ RasMol ]
		Glu H:148 - Pro H:149	[ RasMol ]
		Phe B:146 - Pro B:147	[ RasMol ]
		Phe H:146 - Pro H:147	[ RasMol ]
		Thr A:7 - Pro A:8	[ RasMol ]
		Thr L:7 - Pro L:8	[ RasMol ]
		Tyr A:140 - Pro A:141	[ RasMol ]
		Tyr L:140 - Pro L:141	[ RasMol ]
		Val A:94 - Pro A:95	[ RasMol ]
		Val L:94 - Pro L:95	[ RasMol ]

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	1fl6
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1fl5	THE UNLIGANDED GERMLINE PRECURSOR TO CATALYTIC ANTIBODY 28B4
1kel	THE HAPTEN BOUND CATALYTIC ANTIBODY 28B4
1kem	THE UNLIGANDED CATALYTIC ANTIBODY 28B4

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

SS Bonds (8, 8)

Cis Peptide Bonds (10, 10)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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SCOP Domains (4, 8)

CATH Domains (1, 8)

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