1FL5 - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   THE UNLIGANDED GERMLINE PRECURSOR TO THE 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 :   2.10

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 ANTIBODY 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
	Synonym	:	IF KAPPA LIGHT CHAIN

Molecule 2 - ANTIBODY GERMLINE PRECURSOR TO ANTIBODY 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
	Synonym	:	IGG1 HEAVY CHAIN

		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	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	SO4	1	Ligand/Ion	SULFATE ION

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	PHE B:27 , THR B:28 , ASP B:31 , TYR B:32 , TYR H:33 , ARG H:52	BINDING SITE FOR RESIDUE SO4 H 301
2	AC2	SOFTWARE	TYR B:33 , PHE B:50 , ARG B:52 , PHE H:27 , THR H:28	BINDING SITE FOR RESIDUE SO4 B 302

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 1FL5)

(no "PROSITE Motif" information available for 1FL5)

(no "Exon" information available for 1FL5)

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 d1fl5a1 A:1-107 Immunoglobulin light chain kappa variable domain, VL-kappa                                      d1fl5a2 A:108-212 Immunoglobulin light chain kappa constant domain, CL-kappa                              SCOP domains
               CATH domains --1fl5A01 A:3-108 Immunoglobulins                                                                                1fl5A02 A:109-211 Immunoglobulins                                                                      - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee....eeeeeeee............eeeeee......eeeee...ee.......eeeeee..eeeeeee..hhhhheeeeeee......ee...eeeee.......eeeee..hhhhhh..eeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhhhh.eeeeeee.......eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1fl5 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 d1fl5b1 B:1-113 Immunoglobulin heavy chain variable domain, VH                                                         d1fl5b2 B:114-213 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                      SCOP domains
               CATH domains 1fl5B01 B:1-113 Immunoglobulins                                                                                        1fl5B02 B:114-213 Immunoglobulins                                                                    CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee..hhhhh.eeeeee......eeeeee.hhhhh..eee.......eeeeee....eeeeee...hhhhheeeeeee............eeeee........eeeee..........eeeeeeeeeee.....eeee........eee...ee.....eeeeeeeeee.hhh.....eeeeeehhhheeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1fl5 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 d1fl5h1 H:1-113 Immunoglobulin heavy chain variable domain, VH                                                         d1fl5h2 H:114-213 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                      SCOP domains
               CATH domains 1fl5H01 H:1-113 Immunoglobulins                                                                                        1fl5H02 H:114-213 Immunoglobulins                                                                    CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee..hhhhh.eeeeee......eeeeee.hhhhh..eee.......eeeeee....eeeeee...hhhhheeeeeee............eeeee........eeeee..........eeeeeeeeeee.....eeee........eee...ee.....eeeeeeeeee.hhh.....eeeeeehhhheeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1fl5 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 d1fl5l1 L:1-107 Immunoglobulin light chain kappa variable domain, VL-kappa                                      d1fl5l2 L:108-212 Immunoglobulin light chain kappa constant domain, CL-kappa                              SCOP domains
               CATH domains --1fl5L01 L:3-108 Immunoglobulins                                                                                1fl5L02 L:109-211 Immunoglobulins                                                                      - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeeee...eeeeeeee............eeeeee......eeeee...ee.......eeeeee..eeeeeee..hhhhheeeeeee......ee...eeeeee......eeeee..hhhhhh..eeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhhhh.eeeeeee.......eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1fl5 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( (-)

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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	1fl5A02	A:109-211
1b	1fl5A01	A:3-108
1c	1fl5L01	L:3-108
1d	1fl5B02	B:114-213
1e	1fl5H02	H:114-213
1f	1fl5B01	B:1-113
1g	1fl5H01	H:1-113
1h	1fl5L02	L:109-211

(no "Pfam Domain" information available for 1FL5)

Asymmetric Unit(hide GO term definitions)

(no "Gene Ontology" information available for 1FL5)

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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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1kel	THE HAPTEN BOUND STRUCTURE OF THE AFFINITY-MATURED CATALYTIC ANTIBODY 28B4
1kem	THE UNLIGANDED STRUCTURE OF THE AFFINITY-MATURED 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)

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