1LO3 - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   RETRO-DIELS-ALDERASE CATALYTIC ANTIBODY: PRODUCT ANALOGUE

Authors :   M. Hugot, J. L. Reymond, U. Baumann

Date :   06 May 02 (Deposition) - 03 Jul 02 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

Chains :   Asym. Unit : H,L,X,Y
Biol. Unit 1: X,Y  (1x)
Biol. Unit 2: H,L  (1x)

Keywords :   Fab, Catalytic Antibody, Product Complex, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Hugot, N. Bensel, M. Vogel, M. T. Reymond, B. Stadler, J. L. Reymond, U. Baumann
A Structural Basis For The Activity Of Retro-Diels-Alder Catalytic Antibodies: Evidence For A Catalytic Aromatic Residue.
Proc. Natl. Acad. Sci. Usa V. 99 9674 2002
PubMed-ID: 12093912 | Reference-DOI: 10.1073/PNAS.142286599
(for further references see the PDB file header)

Molecule 1 - IF KAPPA LIGHT CHAIN
	Chains	:	X, L
	Fragment	:	FAB FRAGMENT
	Organism Common	:	HOUSE MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Other Details	:	THE ANTIBODIES WERE ISOLATED FROM HYBRIDOMA CELLS AND FAB FRAGMENTS WERE GENERATED BY PAPAIN DIGESTION.
	Synonym	:	CATALYTIC ANTIBODY 9D9

Molecule 2 - IG GAMMA 2A HEAVY CHAIN
	Chains	:	Y, H
	Organism Common	:	HOUSE MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Other Details	:	THE ANTIBODIES WERE ISOLATED FROM HYBRIDOMA CELLS AND FAB FRAGMENTS WERE GENERATED BY PAPAIN DIGESTION.

		1	2	3	4
Asymmetric Unit	:	H	L	X	Y
Biological Unit 1 (1x)	:			X	Y
Biological Unit 2 (1x)	:	H	L

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 2)

No.	Name	Count	Type	Full Name
1	AN1	2	Ligand/Ion	3-(10-METHYL-ANTHRACEN-9-YL)-PROPIONIC ACID

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	AN1	1	Ligand/Ion	3-(10-METHYL-ANTHRACEN-9-YL)-PROPIONIC ACID

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	AN1	1	Ligand/Ion	3-(10-METHYL-ANTHRACEN-9-YL)-PROPIONIC ACID

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS X:31 , TYR X:37 , PHE X:99 , GLY Y:33 , ILE Y:51 , SER Y:52 , ASP Y:102 , PHE Y:104 , LEU Y:104A , VAL Y:104B , TRP Y:105 , HOH Y:523	BINDING SITE FOR RESIDUE AN1 Y 500
2	AC2	SOFTWARE	GLY H:33 , ILE H:51 , SER H:52 , TYR H:61 , ASP H:102 , PHE H:104 , LEU H:104A , VAL H:104B , TRP H:105 , TYR L:37 , PHE L:99	BINDING SITE FOR RESIDUE AN1 H 501

Asymmetric Unit

No.	Residues
1	H:22	-	H:98
2	H:146	-	H:201
3	L:23	-	L:93
4	L:139	-	L:199
5	L:220	-	H:134
6	X:23	-	X:93
7	X:139	-	X:199
8	X:220	-	Y:134
9	Y:22	-	Y:98
10	Y:146	-	Y:201

Asymmetric Unit

No.	Residues
1	Thr X:7	-	Pro X:8
2	Phe X:99	-	Pro X:100
3	Tyr X:145	-	Pro X:146
4	Phe Y:152	-	Pro Y:153
5	Glu Y:154	-	Pro Y:155
6	Trp Y:194	-	Pro Y:195
7	Thr L:7	-	Pro L:8
8	Phe L:99	-	Pro L:100
9	Tyr L:145	-	Pro L:146
10	Phe H:152	-	Pro H:153
11	Glu H:154	-	Pro H:155
12	Trp H:194	-	Pro H:195

(no "SAP(SNP)/Variant" information available for 1LO3)

(no "PROSITE Motif" information available for 1LO3)

(no "Exon" information available for 1LO3)

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 H from PDB  Type:PROTEIN  Length:220
 aligned with Q91Z05_MOUSE | Q91Z05 from UniProtKB/TrEMBL  Length:473

    Alignment length:221
                                                                                                                             118                                                                                                                         
                                                                                                                           117 |                                                                                                                         
                                    29        39        49        59        69        79        89        99       109       118       128       138       148       158       168       178       188       198       208       218       228       238 
        Q91Z05_MOUSE     20 EVQLVESGGGLVKPGGSRKLSCAASGFTFSDYGMHWVRQAPEKGLEWVAYINSGSTTIYYADTVKGRFTISRDNAKNTLFLQMTSLRSEDTAMYYCAR-ELWLRRIDYWGQGTTITVSSAKTTPPSVYPLAPGCGDTTGSSVTLGCLVKGYFPESVTVTWNSGSLSSSVHTFPALLQSGLYTMSSSVTVPSSTWPSQTVTCSVAHPASSTTVDKKLEPSGP  239
               SCOP domains d1lo3h1 H:1-119 Immunoglobulin heavy chain variable d omain, VH                                                        d1lo3h2 H:120-221 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                        SCOP domains
               CATH domains 1lo3H01 H:1-119 Immunoglobulins                                                                                        1lo3H02 H:120-218 Immunoglobulins                                                                  --- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee..hhhhheeeeeee.....eeeeeee..-...ee........eeeeee....eeeeee........eeeeeeeee............eeeee........eeeee..........eeeeeeeeeee.....eeee.hhh....eee...ee....eeeeeeeeee.........eeeeeehhhheeeeee...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1lo3 H    1 EVKLVESGGGLVKPGGSLKLSCAASGFSFRNYGMSWVRQTPEKRLEWVASISY-GGLIYYPDSIKGRFTISRDIAQNILYLQMSSLRSEDTAMYHCIRGDSFLVWFTFWGQGTLVTVSAAKTTAPSVYPLAPVCGDTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVTSSTWPSQSITCNVAHPASSTQVDKKIEPRGP  221
                                    10        20        30        40        50  | |   62        72        82        92       102  ||   110       120       130       140       150       160       170       180       190       200       210       220 
                                                                               53 |                                            104A|                                                                                                                     
                                                                                 57                                             104B

Chain L from PDB  Type:PROTEIN  Length:219
 aligned with Q65ZC0_MOUSE | Q65ZC0 from UniProtKB/TrEMBL  Length:219

    Alignment length:219
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210         
        Q65ZC0_MOUSE      1 ELVMTQSPLSLSVSLGDQASISCRSSQSLVHTNGNTYLHWYLQKPGLSPKLLIYIVSNRFSGVPDRFSGSGSGTDFTLKISRVEAEDLGVYFCSQSTHVPGTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRGEC  219
               SCOP domains d1lo3l1 L:1-112 Immunoglobulin light chain kappa variable domain, VL-kappa                                      d1lo3l2 L:113-220 Immunoglobulin light chain kappa constant domain, CL-kappa                                SCOP domains
               CATH domains 1lo3L01 L:1-113 Immunoglobulins                                                                                  1lo3L02 L:114-216 Immunoglobulins                                                                      --- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee............eeeeee.....eeeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee......ee...eeeee.......eeeee..hhhhhhh.eeeeeeeeeee....eeeeeee..ee....eeeee.........eeeeeeeeeehhhhhh..eeeeeeee......eeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1lo3 L    1 DVLMTQTPLSLPVSLGDQVSIFCTSSQTIVHTNGNTYLEWYLQKPGQSPKLLIYKVSNRFSGVPDRFSGSGSGTDFTLKISRVETEDLGIYYCFQGSHFPLAFGAGTKLELKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC  220
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       ||
                                                                                                                                                                                                                                                   218|
                                                                                                                                                                                                                                                    220

Chain X from PDB  Type:PROTEIN  Length:219
 aligned with Q65ZC0_MOUSE | Q65ZC0 from UniProtKB/TrEMBL  Length:219

    Alignment length:219
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210         
        Q65ZC0_MOUSE      1 ELVMTQSPLSLSVSLGDQASISCRSSQSLVHTNGNTYLHWYLQKPGLSPKLLIYIVSNRFSGVPDRFSGSGSGTDFTLKISRVEAEDLGVYFCSQSTHVPGTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRGEC  219
               SCOP domains d1lo3x1 X:1-112 Immunoglobulin light chain kappa variable domain, VL-kappa                                      d1lo3x2 X:113-220 Immunoglobulin light chain kappa constant domain, CL-kappa                                SCOP domains
               CATH domains 1lo3X01 X:1-113 Immunoglobulins                                                                                  1lo3X02 X:114-216 Immunoglobulins                                                                      --- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee............eeeeee.....eeeeee...ee.......eeeeee..eeeeee.........eeeeee......ee...eeeee.......eeeee..hhhhhhhheeeeeeeeeee....eeeeeee........eeeee.........eeeeeeeeeehhhhh...eeeeeeee......eeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1lo3 X    1 DVLMTQTPLSLPVSLGDQVSIFCTSSQTIVHTNGNTYLEWYLQKPGQSPKLLIYKVSNRFSGVPDRFSGSGSGTDFTLKISRVETEDLGIYYCFQGSHFPLAFGAGTKLELKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC  220
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       ||
                                                                                                                                                                                                                                                   218|
                                                                                                                                                                                                                                                    220

Chain Y from PDB  Type:PROTEIN  Length:220
 aligned with Q91Z05_MOUSE | Q91Z05 from UniProtKB/TrEMBL  Length:473

    Alignment length:221
                                                                                                                             118                                                                                                                         
                                                                                                                           117 |                                                                                                                         
                                    29        39        49        59        69        79        89        99       109       118       128       138       148       158       168       178       188       198       208       218       228       238 
        Q91Z05_MOUSE     20 EVQLVESGGGLVKPGGSRKLSCAASGFTFSDYGMHWVRQAPEKGLEWVAYINSGSTTIYYADTVKGRFTISRDNAKNTLFLQMTSLRSEDTAMYYCAR-ELWLRRIDYWGQGTTITVSSAKTTPPSVYPLAPGCGDTTGSSVTLGCLVKGYFPESVTVTWNSGSLSSSVHTFPALLQSGLYTMSSSVTVPSSTWPSQTVTCSVAHPASSTTVDKKLEPSGP  239
               SCOP domains d1lo3y1 Y:1-119 Immunoglobulin heavy chain variable d omain, VH                                                        d1lo3y2 Y:120-221 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                        SCOP domains
               CATH domains 1lo3Y01 Y:1-119 Immunoglobulins                                                                                        1lo3Y02 Y:120-218 Immunoglobulins                                                                  --- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee..hhhhheeeeeee.....eeeeeee..-...ee........eeeeee....eeeeee...hhhhheeeeeeeee............eeeee........eeeee..........eeeeeeeeeee.....eeee.hhh....eee...ee....eeeeeeeeee.........eeeeeehhhheeeeee...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1lo3 Y    1 EVKLVESGGGLVKPGGSLKLSCAASGFSFRNYGMSWVRQTPEKRLEWVASISY-GGLIYYPDSIKGRFTISRDIAQNILYLQMSSLRSEDTAMYHCIRGDSFLVWFTFWGQGTLVTVSAAKTTAPSVYPLAPVCGDTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVTSSTWPSQSITCNVAHPASSTQVDKKIEPRGP  221
                                    10        20        30        40        50  | |   62        72        82        92       102  ||   110       120       130       140       150       160       170       180       190       200       210       220 
                                                                               53 |                                            104A|                                                                                                                     
                                                                                 57                                             104B

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(

)

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	1lo3L02	L:114-216
1b	1lo3H02	H:120-218
1c	1lo3Y02	Y:120-218
1d	1lo3L01	L:1-113
1e	1lo3X01	X:1-113
1f	1lo3H01	H:1-119
1g	1lo3Y01	Y:1-119
1h	1lo3X02	X:114-216

(no "Pfam Domain" information available for 1LO3)

Asymmetric Unit(hide GO term definitions)

(no "Gene Ontology" information available for 1LO3)

Asymmetric Unit
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	Cis Peptide Bonds
		Glu H:154 - Pro H:155	[ RasMol ]
		Glu Y:154 - Pro Y:155	[ RasMol ]
		Phe H:152 - Pro H:153	[ RasMol ]
		Phe L:99 - Pro L:100	[ RasMol ]
		Phe X:99 - Pro X:100	[ RasMol ]
		Phe Y:152 - Pro Y:153	[ RasMol ]
		Thr L:7 - Pro L:8	[ RasMol ]
		Thr X:7 - Pro X:8	[ RasMol ]
		Trp H:194 - Pro H:195	[ RasMol ]
		Trp Y:194 - Pro Y:195	[ RasMol ]
		Tyr L:145 - Pro L:146	[ RasMol ]
		Tyr X:145 - Pro X:146	[ RasMol ]

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		Biological Unit 2	[ Jena3D ]

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	1lo3
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	Q65ZC0_MOUSE \| Q65ZC0
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		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/TrEMBL
	Q91Z05_MOUSE \| Q91Z05
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	Q91Z05_MOUSE \| Q91Z05
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UniProtKB/Swiss-Prot
	Q65ZC0_MOUSE \| Q65ZC0	:	2g60
UniProtKB/TrEMBL
	Q65ZC0_MOUSE \| Q65ZC0	:	1i9i 1i9j 1l7t 1lo2 1lo4 1t66 2gjz 2gk0
	Q91Z05_MOUSE \| Q91Z05	:	1i9i 1i9j 1jgu 1jgv 1l7t 1lo2 1lo4 1t66 2gk0

1l00	CATALYTIC RETRO-DIELS-ALDERASE TRANSITION STATE ANALOGUE COMPLEX
1l02	RETRO-DIELS-ALDERASE CATALYTIC ANTIBODY
1l06	RETRO-DIELS-ALDERASE CATALYTIC ANTIBODY 9D9

Description

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Ligands, Modified Residues, Ions (1, 2)

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SS Bonds (10, 10)

Cis Peptide Bonds (12, 12)

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