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(-) Description

Title :  STRUCTURE OF A CATALYTIC ANTIBODY IGG2A FAB FRAGMENT (D2.4)
 
Authors :  B. Golinelli-Pimpaneau, M. Knossow
Date :  15 Apr 97  (Deposition) - 15 Oct 97  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.10
Chains :  Asym. Unit :  A,B,H,L
Biol. Unit 1:  H,L  (1x)
Biol. Unit 2:  A,B  (1x)
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)

(-) Compounds

Molecule 1 - IGG1 FAB FRAGMENT (D.2.4)
    Chains: L, A
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Other Details: TRANSITION STATE ANALOGUE
 
Molecule 2 - IGG1 FAB FRAGMENT (D.2.4)
    Chains: H, B
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Other Details: TRANSITION STATE ANALOGUE

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABHL
Biological Unit 1 (1x):   HL
Biological Unit 2 (1x): AB  

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1PNB2Ligand/Ion4-NITRO-BENZYLPHOSPHONOBUTANOYL-GLYCINE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1PNB1Ligand/Ion4-NITRO-BENZYLPHOSPHONOBUTANOYL-GLYCINE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1PNB1Ligand/Ion4-NITRO-BENZYLPHOSPHONOBUTANOYL-GLYCINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU H:37 , TRP H:95 , PHE H:97 , TYR H:100E , TRP H:103 , TYR L:32 , ASN L:34 , VAL L:89 , GLY L:91 , TYR L:96 , PHE L:98 , HOH L:552BINDING SITE FOR RESIDUE PNB L 551
2AC2SOFTWARETYR A:32 , ASN A:34 , VAL A:89 , GLY A:91 , TYR A:96 , PHE A:98 , LEU B:37 , TRP B:95 , PHE B:97 , TYR B:100E , TRP B:103BINDING SITE FOR RESIDUE PNB A 552

(-) SS Bonds  (8, 8)

Asymmetric Unit
No.Residues
1A:23 -A:88
2A:137 -A:197
3B:22 -B:92
4B:142 -B:197
5H:22 -H:92
6H:142 -H:197
7L:23 -L:88
8L:137 -L:197

(-) Cis Peptide Bonds  (8, 8)

Asymmetric Unit
No.Residues
1Ser L:7 -Pro L:8
2Tyr L:143 -Pro L:144
3Ser A:7 -Pro A:8
4Tyr A:143 -Pro A:144
5Phe H:148 -Pro H:149
6Glu H:150 -Pro H:151
7Phe B:148 -Pro B:149
8Glu B:150 -Pro B:151

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1YED)

(-) Sequences/Alignments

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:219
                                                                                                                                                                                                                                                            
               SCOP domains d1yeda1 A:1-107 Immunoglobulin light chain kappa variable domain, VL-kappa                                      d1yeda2 A:111-222 Immunoglobulin light chain kappa constant domain, CL-kappa                                SCOP domains
               CATH domains 1yedA01 A:1-111 Immunoglobulins                                                                                  1yedA02 A:112-222 Immunoglobulins                                                                          CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
     Sec.struct. author (1) ...eeee..eeeee....eeeeeee............eeee.........................eeeeee..eeeeee....hhh.eeeeeee...........eeeeee......eeeee...hhhhhh.eeeeeeeeeee.....-----hhh......eeeee.........eeeeeeeeeehhhhhh..eeeeeee......eeeeeee.... Sec.struct. author (1)
     Sec.struct. author (2) -----------------------------------------------------------------------------------------------------------------------------------------------------eeeeee---------------------------------------------------------------- Sec.struct. author (2)
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1yed A    1 DIVMTQSPLTLSVTIGQPASISCKSSQSLLYSNGKTYLNWLLQRPGQSPKRLIYLVSKLESGVPDRFTGSGSGTDFTLKISRVEAADLGVYYCVQGTHFPYTFGGGTKLEILRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC  222
                                    10        20       27C||      35        45        55        65        75        85        95       105 ||    118       128       138       148       158       168       178       188       198       208     ||  
                                                     27A||||                                                                             107|                                                                                                    214|  
                                                      27B|||                                                                              111                                                                                                     220  
                                                       27C||                                                                                                                                                                                           
                                                        27D|                                                                                                                                                                                           
                                                         27E                                                                                                                                                                                           


Chain B from PDB  Type:PROTEIN  Length:226
                                                                                                                                                                                                                                                                   
               SCOP domains d1yedb1 B:1-113 Immunoglobulin heavy chain variable domain, VH                                                              d1yedb2 B:116-217 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                        SCOP domains
               CATH domains 1yedB01 B:1-113 Immunoglobulins                                                                                             1yedB02 B:116-214 Immunoglobulins                                                                  --- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee....eeeeeeeee...hhh.eeeeeee......eeeeeee....eeee.hhh...eeeeee....eeeeeee...hhh.eeeeee....................eeeee........eeeee..........eeeeeeeeeee.....eeeehhh.....eeee........eeeeeeeeeehhh......eeeeeehhh.eeeeee...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1yed B    1 AVKLQQSGPELVRPGTSVKLSCKTSGYIFTSYWIHWLKQSSGQGLEWIARIYPGTGGTYYNEKFKGKATLTADKSSSTAYMQLSSLKSEDSAVYFCTRWGFTTVRENYYAMDYWGQGTLVTVSSAKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSPRPSETVTCNVAHPASSTKVDKKIVPRDC  217
                                    10        20        30        40        50  |     59        69        79   |||  86        96    ||100F|      109   ||  121       131       141       151       161       171       181       191       201       211      
                                                                              52A                            82A||               100A||||||          113|                                                                                                     
                                                                                                              82B|                100B|||||           116                                                                                                     
                                                                                                               82C                 100C||||                                                                                                                   
                                                                                                                                    100D|||                                                                                                                   
                                                                                                                                     100E||                                                                                                                   
                                                                                                                                      100F|                                                                                                                   
                                                                                                                                       100G                                                                                                                   


Chain H from PDB  Type:PROTEIN  Length:226
                                                                                                                                                                                                                                                                   
               SCOP domains d1yedh1 H:1-113 Immunoglobulin heavy chain variable domain, VH                                                              d1yedh2 H:116-217 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                        SCOP domains
               CATH domains 1yedH01 H:1-113 Immunoglobulins                                                                                             1yedH02 H:116-214 Immunoglobulins                                                                  --- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee....eeeeeeeee...hhh.eeeeeee......eeeeeee....eeee.hhh...eeeeee....eeeeeee...hhh.eeeeee....................eeeee........eeeee..........eeeeeeeeeee.....eeeehhh.....eeee........eeeeeeeeeehhh......eeeeeehhh.eeeeee...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1yed H    1 AVKLQQSGPELVRPGTSVKLSCKTSGYIFTSYWIHWLKQSSGQGLEWIARIYPGTGGTYYNEKFKGKATLTADKSSSTAYMQLSSLKSEDSAVYFCTRWGFTTVRENYYAMDYWGQGTLVTVSSAKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSPRPSETVTCNVAHPASSTKVDKKIVPRDC  217
                                    10        20        30        40        50  |     59        69        79   |||  86        96    ||100F|      109   ||  121       131       141       151       161       171       181       191       201       211      
                                                                              52A                            82A||               100A||||||          113|                                                                                                     
                                                                                                              82B|                100B|||||           116                                                                                                     
                                                                                                               82C                 100C||||                                                                                                                   
                                                                                                                                    100D|||                                                                                                                   
                                                                                                                                     100E||                                                                                                                   
                                                                                                                                      100F|                                                                                                                   
                                                                                                                                       100G                                                                                                                   


Chain L from PDB  Type:PROTEIN  Length:219
                                                                                                                                                                                                                                                            
               SCOP domains d1yedl1 L:1-107 Immunoglobulin light chain kappa variable domain, VL-kappa                                      d1yedl2 L:111-222 Immunoglobulin light chain kappa constant domain, CL-kappa                                SCOP domains
               CATH domains 1yedL01 L:1-111 Immunoglobulins                                                                                  1yedL02 L:112-222 Immunoglobulins                                                                          CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
     Sec.struct. author (1) ...eeee..eeeee....eeeeeee............eeee.........................eeeeee..eeeeee....hhh.eeeeeee...........eeeeee......eeeee...hhhhhh.eeeeeeeeeee.....-----hhh......eeeee.........eeeeeeeeeehhhhhh..eeeeeee......eeeeeee.... Sec.struct. author (1)
     Sec.struct. author (2) -----------------------------------------------------------------------------------------------------------------------------------------------------eeeeee---------------------------------------------------------------- Sec.struct. author (2)
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1yed L    1 DIVMTQSPLTLSVTIGQPASISCKSSQSLLYSNGKTYLNWLLQRPGQSPKRLIYLVSKLESGVPDRFTGSGSGTDFTLKISRVEAADLGVYYCVQGTHFPYTFGGGTKLEILRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC  222
                                    10        20       27C||      35        45        55        65        75        85        95       105 ||    118       128       138       148       158       168       178       188       198       208     ||  
                                                     27A||||                                                                             107|                                                                                                    214|  
                                                      27B|||                                                                              111                                                                                                     220  
                                                       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 '|'

 Classification and Annotation

(-) SCOP Domains  (4, 8)

Asymmetric Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 8)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)
(-)
Architecture: Sandwich (5577)
(-)
Topology: Immunoglobulin-like (3897)
(-)
Homologous Superfamily: Immunoglobulins (2282)
(-)
House mouse (Mus musculus) (616)
1a1yedA02A:112-222
1b1yedA01A:1-111
1c1yedL01L:1-111
1d1yedB02B:116-214
1e1yedH02H:116-214
1f1yedL02L:112-222
1g1yedB01B:1-113
1h1yedH01H:1-113

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (17, 17)

Asymmetric Unit(hide GO term definitions)

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  1yed
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  IGHG1_MOUSE | P01868
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        IGHG1_MOUSE | P01868: 1ahw 1ai1 1bm3 1clo 1ct8 1dba 1dbb 1dbj 1dbk 1dbm 1emt 1fbi 1fdl 1fns 1gpo 1k4d 1kel 1kem 1mf2 1mlc 1n5y 1n6q 1ntl 1oak 1opg 1p2c 1p7k 1r0a 1r3i 1r3j 1r3k 1r3l 1rih 1seq 1t2q 2aty 2b2x 2dbl 3zo0

(-) Related Entries Specified in the PDB File

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