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Asym./Biol. Unit (Jmol Viewer)

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Title :   STRUCTURE OF A CATALYTIC ANTIBODY, IGG2A FAB FRAGMENT (D2.5)

Authors :   B. Golinelli-Pimpaneau, M. Knossow

Date :   15 Apr 97 (Deposition) - 15 Oct 97 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

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

Keywords :   Catalytic Antibody, Transition State Analogue (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. B. Charbonnier, B. Golinelli-Pimpaneau, B. Gigant, D. S. Tawfik, R. Chap, D. G. Schindler, S. H. Kim, B. S. Green, Z. Eshhar, M. Knossow
Structural Convergence In The Active Sites Of A Family Of Catalytic Antibodies.
Science V. 275 1140 1997
PubMed-ID: 9027317 | Reference-DOI: 10.1126/SCIENCE.275.5303.1140
(for further references see the PDB file header)

Molecule 1 - IGG2A FAB FRAGMENT (D2.5)
	Chains	:	L
	Organism Common	:	HOUSE MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Other Details	:	TRANSITION STATE ANALOGUE

Molecule 2 - IGG2A FAB FRAGMENT (D2.5)
	Chains	:	H
	Organism Common	:	HOUSE MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Other Details	:	TRANSITION STATE ANALOGUE

		1	2
Asymmetric/Biological Unit	:	H	L

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 1)

No.	Name	Count	Type	Full Name
1	PNB	1	Ligand/Ion	4-NITRO-BENZYLPHOSPHONOBUTANOYL-GLYCINE

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS H:35 , TRP H:95 , PHE H:97 , TYR H:100D , HOH H:580 , TYR L:27D , VAL L:89 , GLY L:91 , TYR L:96 , PHE L:98	BINDING SITE FOR RESIDUE PNB H 551

Asymmetric/Biological Unit

No.	Residues
1	H:22	-	H:92
2	H:140	-	H:206
3	L:23	-	L:88
4	L:134	-	L:194

Asymmetric/Biological Unit

No.	Residues
1	Ser L:7	-	Pro L:8
2	Phe 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	Trp H:197	-	Pro H:198

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

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

(no "Exon" information available for 1YEE)

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:222
                                                                                                                                                                                                                                                               
               SCOP domains d1yeeh1 H:1-113 Immunoglobulin heavy chain variable domain, VH                                                             d1yeeh2 H:114-223 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                     SCOP domains
               CATH domains 1yeeH01 H:1-113 Immunoglobulins                                                                                            1yeeH02 H:114-223 Immunoglobulins                                                                   CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee...hhh.eeeeeeee...eeeeeeeee....eeee.hhh...eeeeee....eeeeee....hhh.eeeeee...................eeeee........eeeee..........eeeeeeeeeee.....eeeehhh.....eee...eee..eeeeeeeeeee.........eeeeeehhh.eeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                1yee H    1 EVKLQESGAELVRPGASVKLSCKTSGYIFTSYWIHWVKQRAAAGLEWIARIYPGTGSSYYNVKFKGKATLTADKSSSTAYMQLSSLKSDDSAVYFCVRWGFIPVREDYVLDYWGQGTLVTVSSAKTTAPSVYPLAPVCGDTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIEP  223
                                    10        20        30        40        50  |     59        69        79   |||  86        96    ||100F       110       120       130       140       150 ||||  165 ||    176 ||    188     ||200   ||  211       221  
                                                                              52A                            82A||               100A|||||                                                 152|||    167|      178|          194| || 204|                 
                                                                                                              82B|                100B||||                                                  154||     169       181           196 ||  206                 
                                                                                                               82C                 100C|||                                                   155|                               198|                      
                                                                                                                                    100D||                                                    160                                200                      
                                                                                                                                     100E|                                                                                                                
                                                                                                                                      100F

Chain L from PDB  Type:PROTEIN  Length:219
                                                                                                                                                                                                                                                            
               SCOP domains d1yeel1 L:1-107 Immunoglobulin light chain kappa variable domain, VL-kappa                                      d1yeel2 L:108-214 Immunoglobulin light chain kappa constant domain, CL-kappa                                SCOP domains
               CATH domains 1yeeL01 L:1-108 Immunoglobulins                                                                                  1yeeL02 L:109-214 Immunoglobulins                                                                          CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeee............eeeeee......eeee.............eeeeee..eeeeee....hhh.eeeeeee...........eeeeee......eeeee...hhhhhh.eeeeeeeee......eeeeeee..eee...eeeee...........eeeeeeeehhhhhh..eeeeeeee......eeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1yee L    1 DIVMTQSPLTLSVTIGQPASISCKSSQSLLYSNGKTYLSWLLQRPGQSPKRLIYLVSKLDSGVPDRFTGSGSGTDFTLKISRVEAADLGLYYCVQGTHFPYTFGGGTKLEILRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC  214
                                    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)
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		→ 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	1yeeL02	L:109-214
1b	1yeeL01	L:1-108
1c	1yeeH02	H:114-223
1d	1yeeH01	H:1-113

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

Asymmetric/Biological Unit(hide GO term definitions)

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Glu H:148 - Pro H:149	[ RasMol ]
		Phe H:146 - Pro H:147	[ RasMol ]
		Phe L:94 - Pro L:95	[ RasMol ]
		Ser L:7 - Pro L:8	[ RasMol ]
		Trp H:197 - Pro H:198	[ RasMol ]
		Tyr L:140 - Pro L:141	[ RasMol ]

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Description

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Ligands, Modified Residues, Ions (1, 1)

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SS Bonds (4, 4)

Cis Peptide Bonds (6, 6)

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