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Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   CATALYTIC ANTIBODY 4B2 IN COMPLEX WITH ITS AMIDINIUM HAPTEN.

Authors :   B. Golinelli-Pimpaneau, O. Goncalves, T. Dintinger, D. Blanchard, M. C. Tellier

Date :   02 Jun 00 (Deposition) - 13 Sep 00 (Release) - 04 Jul 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.87

Chains :   Asym./Biol. Unit : H,J,K,L

Keywords :   Catalytic Antibody, Amidinium, Haptenic Charge, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   B. Golinelli-Pimpaneau, O. Goncalves, T. Dintinger, D. Blanchard, M. Knossow, C. Tellier
Structural Evidence For A Programmed General Base In The Active Site Of A Catalytic Antibody.
Proc. Natl. Acad. Sci. Usa V. 97 9892 2000
PubMed-ID: 10963661 | Reference-DOI: 10.1073/PNAS.97.18.9892
(for further references see the PDB file header)

Molecule 1 - CATALYTIC ANTIBODY 4B2
	Chains	:	L, J
	Fragment	:	LIGHT CHAIN - FAB FRAGMENT
	Organism Common	:	HOUSE MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090

Molecule 2 - CATALYTIC ANTIBODY 4B2
	Chains	:	H, K
	Fragment	:	HEAVY CHAIN - FAB FRAGMENT
	Organism Common	:	HOUSE MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090

		1	2	3	4
Asymmetric/Biological Unit	:	H	J	K	L

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 3)

No.	Name	Count	Type	Full Name
1	SO4	1	Ligand/Ion	SULFATE ION
2	TPM	2	Ligand/Ion	2-(4-AMINOBENZYLAMINO)-3,4,5,6-TETRAHYDROPYRIDINIUM

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	THR K:70 , HIS K:81 , HOH K:444	BINDING SITE FOR RESIDUE SO4 K 402
2	AC2	SOFTWARE	HIS H:35 , ALA H:93 , VAL H:99 , TYR L:32 , GLU L:34 , PHE L:89 , GLY L:91 , TYR L:96	BINDING SITE FOR RESIDUE TPM L 400
3	AC3	SOFTWARE	GLU J:34 , PHE J:89 , GLY J:91 , TYR J:96 , HOH J:404 , HOH J:435 , HIS K:35 , ALA K:93 , VAL K:99	BINDING SITE FOR RESIDUE TPM J 401

Asymmetric/Biological Unit

No.	Residues
1	H:22	-	H:92
2	H:148	-	H:203
3	J:23	-	J:88
4	J:134	-	J:194
5	K:22	-	K:92
6	K:148	-	K:203
7	L:23	-	L:88
8	L:134	-	L:194

Asymmetric/Biological 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:154	-	Pro H:155
5	Glu H:156	-	Pro H:157
6	Trp H:196	-	Pro H:197
7	Thr J:7	-	Pro J:8
8	Val J:94	-	Pro J:95
9	Tyr J:140	-	Pro J:141
10	Phe K:154	-	Pro K:155
11	Glu K:156	-	Pro K:157
12	Trp K:196	-	Pro K:197

(no "SAP(SNP)/Variant" information available for 1F3D)

(no "PROSITE Motif" information available for 1F3D)

(no "Exon" information available for 1F3D)

Asymmetric/Biological 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:217
                                                                                                                                                                                                                                                         
               SCOP domains d1f3dh1 H:1-121 Immunoglobulin heavy chain variable domain, VH                                                     d1f3dh2 H:122-223 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                        SCOP domains
               CATH domains 1f3dH01 H:1-121 Immunoglobulins                                                                                    1f3dH02 H:122-220 Immunoglobulins                                                                  --- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee..hhhhh.eeeeeee...eeeeeeee......eee.hhh...eeeeee....eeeeee...hhhhheeeeeee.....ee...eeeee........eeeee..........eeeeeeeeeee.....eeee.hhh....eee...eee..eeeeeeeeeee.........eeeeeehhhheeeeee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1f3d H   1 EIQLQQSGPELVKPGASVKVSCKASGYSFIDYNIHWVKQSHGKSLEWIGYIVPYSGGTTFNQKFKGKATLTVDKSSSTAFMHLNSLTFEDSAVYYCANDYDGVYWGQGTTLTVSSAKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPRDC 223
                                    10        20        30        40        50  |     59        69        79   |||  86        96  ||   108   ||  126       136       146       156       166       176       186       196       206       216       
                                                                              52A                            82A||               99|       112|                                                                                                      
                                                                                                              82B|               102        121                                                                                                      
                                                                                                               82C

Chain J from PDB  Type:PROTEIN  Length:218
 aligned with A2NHM3_MOUSE | A2NHM3 from UniProtKB/TrEMBL  Length:219

    Alignment length:218
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210        
         A2NHM3_MOUSE     1 DVLMTQTPLSLPVSLGDQASISCRSSQSIVHTNGNTYLEWYLQKPGQSPKLLIYKVSNRFSGVPDRFSGSGSGTDFTLKISRVEAEDLGVYYCFQGSHVPRTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNE 218
               SCOP domains d1f3dj1 J:1-107 Immunoglobulin light chain kappa variable domain, VL-kappa                                      d1f3dj2 J:108-213 Immunoglobulin light chain kappa constant domain, CL-kappa                               SCOP domains
               CATH domains 1f3dJ01 J:1-108 Immunoglobulins                                                                                  1f3dJ02 J:109-207 Immunoglobulins                                                                  ------ CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee............eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee......ee...eeeee.......eeeee..hhhhhh..eeeeeeeeeee.....eeeeee..eee...eeeee.........eeeeeeeeeehhhhhh..eeeeeee.......eeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1f3d J   1 DVLMTQTPLSLPVSLGDQVSISCRSSQSIFHSDGKTYLEWHLQKPGQSPKLLIYKVSKRFSGVPDRFSGSGSGTDFTLKISRVEAEDLGVYYCFQGSHVPYTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNA 213
                                    10        20       27C||      35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205        
                                                     27A||||                                                                                                                                                                                          
                                                      27B|||                                                                                                                                                                                          
                                                       27C||                                                                                                                                                                                          
                                                        27D|                                                                                                                                                                                          
                                                         27E

Chain K from PDB  Type:PROTEIN  Length:215
                                                                                                                                                                                                                                                       
               SCOP domains d1f3dk1 K:1-121 Immunoglobulin heavy chain variable domain, VH                                                     d1f3dk2 K:122-221 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                      SCOP domains
               CATH domains 1f3dK01 K:1-121 Immunoglobulins                                                                                    1f3dK02 K:122-220 Immunoglobulins                                                                  - CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee..hhhhh.eeeeeee...eeeeeeee......eee.hhh...eeeeeehhh.eeeeee...hhhhheeeeeee..........eeeee........eeeee..........eeeeeeeeeee.....eeee.hhh....eee...eee..eeeeeeeeeee.........eeeeeehhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1f3d K   1 EIQLQQSGPELVKPGASVKVSCKASGYSFIDYNIHWVKQSHGKSLEWIGYIVPYSGGTTFNQKFKGKATLTVDKSSSTAFMHLNSLTFEDSAVYYCANDYDGVYWGQGTTLTVSSAKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPR 221
                                    10        20        30        40        50  |     59        69        79   |||  86        96  ||   108   ||  126       136       146       156       166       176       186       196       206       216     
                                                                              52A                            82A||               99|       112|                                                                                                    
                                                                                                              82B|               102        121                                                                                                    
                                                                                                               82C

Chain L from PDB  Type:PROTEIN  Length:218
 aligned with A2NHM3_MOUSE | A2NHM3 from UniProtKB/TrEMBL  Length:219

    Alignment length:218
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210        
         A2NHM3_MOUSE     1 DVLMTQTPLSLPVSLGDQASISCRSSQSIVHTNGNTYLEWYLQKPGQSPKLLIYKVSNRFSGVPDRFSGSGSGTDFTLKISRVEAEDLGVYYCFQGSHVPRTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNE 218
               SCOP domains d1f3dl1 L:1-107 Immunoglobulin light chain kappa variable domain, VL-kappa                                      d1f3dl2 L:108-213 Immunoglobulin light chain kappa constant domain, CL-kappa                               SCOP domains
               CATH domains 1f3dL01 L:1-107 Immunoglobulins                                                                                 1f3dL02 L:108-211 Immunoglobulins                                                                       -- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee............eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee......ee...eeeee.......eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee..eee...eeeee.........eeeeeeeeeehhhhhh..eeeeeee.......eeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1f3d L   1 DVLMTQTPLSLPVSLGDQVSISCRSSQSIFHSDGKTYLEWHLQKPGQSPKLLIYKVSKRFSGVPDRFSGSGSGTDFTLKISRVEAEDLGVYYCFQGSHVPYTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNA 213
                                    10        20       27C||      35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205        
                                                     27A||||                                                                                                                                                                                          
                                                      27B|||                                                                                                                                                                                          
                                                       27C||                                                                                                                                                                                          
                                                        27D|                                                                                                                                                                                          
                                                         27E

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/Biological 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	1f3dL02	L:108-211
1b	1f3dH02	H:122-220
1c	1f3dK02	K:122-220
1d	1f3dL01	L:1-107
1e	1f3dJ01	J:1-108
1f	1f3dH01	H:1-121
1g	1f3dK01	K:1-121
1h	1f3dJ02	J:109-207

(no "Pfam Domain" information available for 1F3D)

Asymmetric/Biological Unit(hide GO term definitions)

(no "Gene Ontology" information available for 1F3D)

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Glu H:156 - Pro H:157	[ RasMol ]
		Glu K:156 - Pro K:157	[ RasMol ]
		Phe H:154 - Pro H:155	[ RasMol ]
		Phe K:154 - Pro K:155	[ RasMol ]
		Thr J:7 - Pro J:8	[ RasMol ]
		Thr L:7 - Pro L:8	[ RasMol ]
		Trp H:196 - Pro H:197	[ RasMol ]
		Trp K:196 - Pro K:197	[ RasMol ]
		Tyr J:140 - Pro J:141	[ RasMol ]
		Tyr L:140 - Pro L:141	[ RasMol ]
		Val J:94 - Pro J:95	[ RasMol ]
		Val L:94 - Pro L:95	[ RasMol ]

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Description

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Chains, Units

Ligands, Modified Residues, Ions (2, 3)

Sites (3, 3)

SS Bonds (8, 8)

Cis Peptide Bonds (12, 12)

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