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(-) Description

Title :  STRUCTURE OF A CATALYTIC ANTIBODY IGG2A FAB FRAGMENT (D2.3)
 
Authors :  B. Golinelli-Pimpaneau, M. Knossow
Date :  15 Apr 97  (Deposition) - 15 Oct 97  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  H,L
Biol. Unit 1:  H,L  (1x)
Biol. Unit 2:  H (1x),L (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 - IGG2A FAB FRAGMENT (D2.3)
    Chains: L
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Other Details: CATALYTIC ANTIBODY, TRANSITION STATE ANALOGUE
 
Molecule 2 - IGG2A FAB FRAGMENT (D2.3)
    Chains: H
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Other Details: CATALYTIC ANTIBODY, TRANSITION STATE ANALOGUE

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : HL
Biological Unit 1 (1x): HL
Biological Unit 2 (1x): H (1x)L (1x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric Unit (2, 8)
No.NameCountTypeFull Name
1PNB1Ligand/Ion4-NITRO-BENZYLPHOSPHONOBUTANOYL-GLYCINE
2ZN7Ligand/IonZINC ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1PNB1Ligand/Ion4-NITRO-BENZYLPHOSPHONOBUTANOYL-GLYCINE
2ZN-1Ligand/IonZINC ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1PNB-1Ligand/Ion4-NITRO-BENZYLPHOSPHONOBUTANOYL-GLYCINE
2ZN-1Ligand/IonZINC ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREZN L:219 , ZN L:221 , HOH L:270 , HOH L:271BINDING SITE FOR RESIDUE ZN L 215
2AC2SOFTWARESER H:112 , ZN L:218 , HOH L:288 , HOH L:300BINDING SITE FOR RESIDUE ZN L 216
3AC3SOFTWAREASP H:100C , HOH H:580 , HIS L:49 , HOH L:264BINDING SITE FOR RESIDUE ZN L 217
4AC4SOFTWAREASP H:181 , HIS L:93 , ZN L:216 , HOH L:258 , HOH L:300BINDING SITE FOR RESIDUE ZN L 218
5AC5SOFTWAREASP L:151 , HIS L:189 , ZN L:215 , ZN L:220 , HOH L:256 , HOH L:270BINDING SITE FOR RESIDUE ZN L 219
6AC6SOFTWAREZN L:219 , ZN L:221 , HOH L:256 , HOH L:272 , HOH L:281 , HOH L:283BINDING SITE FOR RESIDUE ZN L 220
7AC7SOFTWAREASP L:60 , ZN L:215 , ZN L:220 , HOH L:271 , HOH L:272 , HOH L:274BINDING SITE FOR RESIDUE ZN L 221
8AC8SOFTWAREHIS H:35 , VAL H:37 , THR H:93 , TRP H:95 , PHE H:97 , TYR H:100D , TRP H:103 , HOH H:561 , TYR L:27D , ASN L:34 , VAL L:89 , GLY L:91 , PHE L:94 , TYR L:96 , PHE L:98BINDING SITE FOR RESIDUE PNB H 551

(-) SS Bonds  (4, 4)

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

(-) Cis Peptide Bonds  (6, 6)

Asymmetric Unit
No.Residues
1Ser L:7 -Pro L:8
2Phe L:94 -Pro L:95
3Tyr L:140 -Pro L:141
4Phe H:146 -Pro H:147
5Glu H:148 -Pro H:149
6Trp H:197 -Pro H:198

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1YEC)

(-) 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 H from PDB  Type:PROTEIN  Length:222
                                                                                                                                                                                                                                                               
               SCOP domains d1yech1 H:1-113 Immunoglobulin heavy chain variable domain, VH                                                             d1yech2 H:114-223 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                     SCOP domains
               CATH domains 1yecH01 H:1-113 Immunoglobulins                                                                                            1yecH02 H:114-223 Immunoglobulins                                                                   CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee...hhh.eeeeeee.....eeeeeeee....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
                1yec H    1 EMQLQQSGAELLRPGTSVKLSCKTSGYIFTSYWIHWVKQRSGQGLEWIARIYPGTGSTYYNEKFKGKATLTADKSSSTAYMQLSTLKSEDSAVYFCTRWGFIPVREDYVMDYWGQGTLVTVSSAKTTAPSVYPLAPVCGDTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIEP  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 d1yecl1 L:1-107 Immunoglobulin light chain kappa variable domain, VL-kappa                                      d1yecl2 L:108-214 Immunoglobulin light chain kappa constant domain, CL-kappa                                SCOP domains
               CATH domains 1yecL01 L:1-108 Immunoglobulins                                                                                  1yecL02 L:109-214 Immunoglobulins                                                                          CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeee............eeeeee.....eeeee.............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
                1yec L    1 DIVMTQSPLTLSVTIGQPASISCKSSQSLLYSNGKTYLNWLLQRPGQSPKRLIHLVSKLDSGVPDRITGSGSGTDFTLKISRVEAADLGVYYCVQGTHFPYTFGGGTKLEILRGDAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC  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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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (4, 4)

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

(-) CATH Domains  (1, 4)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (12, 12)

Asymmetric Unit(hide GO term definitions)

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  1yec
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  GCAA_MOUSE | P01863
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 Related Entries

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UniProtKB/Swiss-Prot
        GCAA_MOUSE | P01863: 1dqm 1dqq 1ehl 1fe8 1ggi 1igt 1keg 1kn2 1kn4 1kno 1mh5 1mnu 1mpa 1ob1 1pg7 1uyw 1yef 1yeg 1yeh 1yei 1yej 1yek 2ipu 2mpa 2r0w 2r0z 2r29 2r69 2r6p 2vl5 2zch 2zck 2zcl 3bgf 3oz9 3zo0 4f37 5vaa

(-) Related Entries Specified in the PDB File

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