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(-) Description

Title :  CATALYTIC ANTIBODY D2.3 COMPLEX
 
Authors :  B. Gigant, M. Knossow
Date :  13 Aug 98  (Deposition) - 13 Jan 99  (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 (2x),L (2x)
Biol. Unit 3:  H,L  (2x)
Biol. Unit 4:  H (1x),L (1x)
Keywords :  Catalytic Antibody D2. 3 Complex, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. Gigant, J. B. Charbonnier, Z. Eshhar, B. S. Green, M. Knossow
Crossreactivity, Efficiency And Catalytic Specificity Of An Esterase-Like Antibody.
J. Mol. Biol. V. 284 741 1998
PubMed-ID: 9826512  |  Reference-DOI: 10.1006/JMBI.1998.2198
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEIN (IG ANTIBODY D2.3 (LIGHT CHAIN))
    Chains: L
    Fragment: ANTIGEN BINDING DOMAIN
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
 
Molecule 2 - PROTEIN (IG ANTIBODY D2.3 (HEAVY CHAIN))
    Chains: H
    Fragment: ANTIGEN BINDING DOMAIN
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : HL
Biological Unit 1 (1x): HL
Biological Unit 2 (2x): H (2x)L (2x)
Biological Unit 3 (2x): HL
Biological Unit 4 (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
1PGG1Ligand/IonPARA-NITROPHENYLPHOSPHONOBUTANOYL-GLYCINE
2ZN7Ligand/IonZINC ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1PGG1Ligand/IonPARA-NITROPHENYLPHOSPHONOBUTANOYL-GLYCINE
2ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1PGG2Ligand/IonPARA-NITROPHENYLPHOSPHONOBUTANOYL-GLYCINE
2ZN-1Ligand/IonZINC ION
Biological Unit 3 (1, 2)
No.NameCountTypeFull Name
1PGG2Ligand/IonPARA-NITROPHENYLPHOSPHONOBUTANOYL-GLYCINE
2ZN-1Ligand/IonZINC ION
Biological Unit 4 (1, 1)
No.NameCountTypeFull Name
1PGG1Ligand/IonPARA-NITROPHENYLPHOSPHONOBUTANOYL-GLYCINE
2ZN-1Ligand/IonZINC ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP L:151 , HIS L:189 , ZN L:605 , ZN L:606 , HOH L:684 , HOH L:686BINDING SITE FOR RESIDUE ZN L 603
2AC2SOFTWARESER H:112 , ASP H:181 , ZN L:602 , HOH L:619 , HOH L:666BINDING SITE FOR RESIDUE ZN L 607
3AC3SOFTWAREASP H:100C , HOH H:292 , HIS L:49 , HOH L:629BINDING SITE FOR RESIDUE ZN L 601
4AC4SOFTWAREASP H:181 , HIS L:93 , ZN L:607 , HOH L:619 , HOH L:682BINDING SITE FOR RESIDUE ZN L 602
5AC5SOFTWAREASP L:60 , ZN L:605 , ZN L:606 , HOH L:608 , HOH L:683 , HOH L:685BINDING SITE FOR RESIDUE ZN L 604
6AC6SOFTWAREZN L:603 , ZN L:604 , HOH L:684 , HOH L:685BINDING SITE FOR RESIDUE ZN L 605
7AC7SOFTWAREZN L:603 , ZN L:604 , HOH L:658 , HOH L:679 , HOH L:683 , HOH L:686BINDING SITE FOR RESIDUE ZN L 606
8AC8SOFTWAREHIS H:35 , VAL H:37 , TRP H:95 , PHE H:97 , TYR H:100D , TYR L:27D , ASN L:34 , VAL L:89 , GLY L:91 , PHE L:94 , TYR L:96 , PHE L:98 , HOH L:609BINDING SITE FOR RESIDUE PGG L 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 1YEI)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1YEI)

(-) 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 d1yeih1 H:1-113 Immunoglobulin heavy chain variable domain, VH                                                             d1yeih2 H:114-223 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                     SCOP domains
               CATH domains 1yeiH01 H:1-113 Immunoglobulins                                                                                            1yeiH02 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
                1yei 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
 aligned with Q58EU8_MOUSE | Q58EU8 from UniProtKB/TrEMBL  Length:239

    Alignment length:219
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230         
        Q58EU8_MOUSE     21 DVVMTQTPLTLSVTIGQPASISCKSSQSLLHSNGKTYLNWLLQRPGQSPKLLIYLVSKLESGVPDRFSGSGSGTDFTLKISRVEAEDLGVYYCLQATHFPRTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC  239
               SCOP domains d1yeil1 L:1-107 Immunoglobulin light chain kappa variable domain, VL-kappa                                      d1yeil2 L:108-214 Immunoglobulin light chain kappa constant domain, CL-kappa                                SCOP domains
               CATH domains 1yeiL01 L:1-108 Immunoglobulins                                                                                  1yeiL02 L:109-214 Immunoglobulins                                                                          CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee............eeeeee.....eeeee.............eeeeee..eeeeee....hhh.eeeeeee...........eeeee.......eeeee...hhhhhh.eeeeeeeee......eeeeeee..eee...eeeee...........eeeeeeeehhhhhh..eeeeeeee......eeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1yei L    1 DIVMTQSPLTLSVTIGQPASISCKSSQSLLYSNGKTYLNWLLQRPGQSPKRLIHLVSKLDSGVPDRITGSGSGTDFTLKISRVEAADLGVYYCVQGTHFPYTFGGGTKLEILRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC  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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  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, 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 1YEI)

(-) Gene Ontology  (12, 12)

Asymmetric Unit(hide GO term definitions)
Chain L   (Q58EU8_MOUSE | Q58EU8)

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  1yei
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  Q58EU8_MOUSE | Q58EU8
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 Related Entries

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

UniProtKB/Swiss-Prot
        GCAA_MOUSE | P01863: 1dqm 1dqq 1ehl 1fe8 1ggi 1igt 1keg 1kn2 1kn4 1kno 1mh5 1mnu 1mpa 1ob1 1pg7 1uyw 1yec 1yef 1yeg 1yeh 1yej 1yek 2ipu 2mpa 2r0w 2r0z 2r29 2r69 2r6p 2vl5 2zch 2zck 2zcl 3bgf 3oz9 3zo0 4f37 5vaa
UniProtKB/TrEMBL
        Q58EU8_MOUSE | Q58EU8: 1kn2 1kn4 1ncw 1nd0 1rua 1rum 1yej 1yek 2c1o 2c1p

(-) Related Entries Specified in the PDB File

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