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(-) Description

Title :  MOLECULAR MECHANISM OF ENANTIOSELECTIVE PROTON TRANSFER TO CARBON IN CATALYTIC ANTIBODY 14D9
 
Authors :  U. Baumann, J. L. Reymond
Date :  05 Feb 04  (Deposition) - 27 Feb 04  (Release) - 15 Mar 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.67
Chains :  Asym. Unit :  H,L,U,V,X,Y
Biol. Unit 1:  H,L  (1x)
Biol. Unit 2:  U,V  (1x)
Biol. Unit 3:  X,Y  (1x)
Keywords :  Antibody (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Zheng, U. Baumann, J. L. Reymond
Molecular Mechanism Of Enantioselective Proton Transfer To Carbon In Catalytic Antibody 14D9
Proc. Natl. Acad. Sci. Usa V. 101 3387 2004
PubMed-ID: 14988504  |  Reference-DOI: 10.1073/PNAS.0400263101

(-) Compounds

Molecule 1 - ANTIBODY 14D9
    Chains: H, V, Y
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: TOP10
    Expression System Taxid: 562
    Expression System Vector: PBAD
    Fragment: FAB HEAVY CHAIN, RESIDUES 4-216
    Organism Scientific: MUS MUSCULUS, HOMO SAPIENS
    Organism Taxid: 10090, 9606
 
Molecule 2 - ANTIBODY 14D9
    Chains: L, U, X
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: TOP10
    Expression System Taxid: 562
    Expression System Vector: PBAD
    Fragment: FAB LIGHT CHAIN, RESIDUES 1-212
    Organism Scientific: MUS MUSCULUS, HOMO SAPIENS
    Organism Taxid: 10090, 9606

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : HLUVXY
Biological Unit 1 (1x): HL    
Biological Unit 2 (1x):   UV  
Biological Unit 3 (1x):     XY

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1UWE)

(-) Sites  (0, 0)

(no "Site" information available for 1UWE)

(-) SS Bonds  (12, 12)

Asymmetric Unit
No.Residues
1H:22 -H:95
2H:140 -H:196
3L:23 -L:88
4L:134 -L:194
5U:23 -U:88
6U:134 -U:194
7V:22 -V:95
8V:140 -V:196
9X:23 -X:88
10X:134 -X:194
11Y:22 -Y:95
12Y:140 -Y:196

(-) Cis Peptide Bonds  (15, 15)

Asymmetric Unit
No.Residues
1Phe H:146 -Pro H:147
2Glu H:148 -Pro H:149
3Ser L:7 -Pro L:8
4Tyr L:94 -Pro L:95
5Tyr L:140 -Pro L:141
6Ser U:7 -Pro U:8
7Tyr U:94 -Pro U:95
8Tyr U:140 -Pro U:141
9Phe V:146 -Pro V:147
10Glu V:148 -Pro V:149
11Ser X:7 -Pro X:8
12Tyr X:94 -Pro X:95
13Tyr X:140 -Pro X:141
14Phe Y:146 -Pro Y:147
15Glu Y:148 -Pro Y:149

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1UWE)

(-) 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:218
                                                                                                                                                                                                                                                           
               SCOP domains d1uweh1 H:4-113 Immunoglobulin heavy chain variable domain, VH                                                     d1uweh2 H:114-216 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                         SCOP domains
               CATH domains 1uweH01 H:4-113 Immunoglobulins                                                                                    1uweH02 H:114-214 Immunoglobulins                                                                    -- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee...eee.....eeeeee....hhhhheeeeeee.....eeeeeee.......ee.hhhh..eeeeeehhh.eeeeee...hhhhheeeeeeeee..eeeee...eeeee........eeeee..hhh.ee..eeeeeeeeeee.....eeee.hhh.................eeeeeeeeee.hhhhh...eeeeee....eeeeee...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1uwe H    4 LLAQSGPELVKPGASVKISCAASAYSITDFTIYWVKQSHGDSLEWIGGIDPHNGGGAYNQKFRVKATLTVDTSSSTAYIHLNSLTSEDSAVYYCAIFYGNFFDYWGQGTTVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTAVDKAVEPKSC  216
                             |      12        22        32        42        52|       61        71        81        91      100A||     108       118       128       138       148       158       168       178       188       198       208        
                             |                                              52A                                             100A||                                                                                                                    
                            4A                                                                                               100B|                                                                                                                    
                                                                                                                              100C                                                                                                                    


Chain L from PDB  Type:PROTEIN  Length:213
                                                                                                                                                                                                                                                      
               SCOP domains d1uwel1 L:1-107 Immunoglobulin light chain kappa variable domain, VL-kappa                                  d1uwel2 L:108-212 Immunoglobulin light chain kappa constant domain, CL-kappa                              SCOP domains
               CATH domains -1uweL01 L:1A-108 Immunoglobulins                                                                            1uweL02 L:109-212 Immunoglobulins                                                                        CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee..eeeee....eeeeeee.......eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee......ee...eeeeee......eeeee..hhhhhh..eeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhhhh.eeeeeee.......eeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1uwe L    1 LDNVMTQSPSFMSTSVGDRVSVTCAASQNVGTNVAWYQQKPGQPPKALIYSTSYRYSGVPDRFTGSGSGTDFTLTISNVNSEDLAEYFCQQYNIYPVTFGGGTKLEIKRTVAAPSVFIFPPSAEQLASGTASVVCLLNNFYPREAAVQWKVDNALQSGNSQESVTEQDSADSTYSLSSTLTLSKADYEAHAVYACEVTHQGLSSPVTKSFNRG  212
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209   
                            1A                                                                                                                                                                                                                   


Chain U from PDB  Type:PROTEIN  Length:213
                                                                                                                                                                                                                                                      
               SCOP domains d1uweu1 U:1-107 Immunoglobulin light chain kappa variable domain, VL-kappa                                  d1uweu2 U:108-212 Immunoglobulin light chain kappa constant domain, CL-kappa                              SCOP domains
               CATH domains -1uweU01 U:1A-108 Immunoglobulins                                                                            1uweU02 U:109-212 Immunoglobulins                                                                        CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee..eeeee....eeeeeee.......eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee......ee...eeeeee......eeeee..hhhhhh..eeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhhhh.eeeeeee.......eeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1uwe U    1 LDNVMTQSPSFMSTSVGDRVSVTCAASQNVGTNVAWYQQKPGQPPKALIYSTSYRYSGVPDRFTGSGSGTDFTLTISNVNSEDLAEYFCQQYNIYPVTFGGGTKLEIKRTVAAPSVFIFPPSAEQLASGTASVVCLLNNFYPREAAVQWKVDNALQSGNSQESVTEQDSADSTYSLSSTLTLSKADYEAHAVYACEVTHQGLSSPVTKSFNRG  212
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209   
                            1A                                                                                                                                                                                                                   


Chain V from PDB  Type:PROTEIN  Length:218
                                                                                                                                                                                                                                                           
               SCOP domains d1uwev1 V:4-113 Immunoglobulin heavy chain variable domain, VH                                                     d1uwev2 V:114-216 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                         SCOP domains
               CATH domains 1uweV01 V:4-113 Immunoglobulins                                                                                    1uweV02 V:114-212 Immunoglobulins                                                                  ---- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee...eee.....eeeeeee...hhhhheeeeeeee...eeeeeeee.......ee.hhhh..eeeeeehhh.eeeeee...hhhhheeeeeeeee...eeee...eeeee........eeeee..hhh.ee..eeeeeeeeeee.....eeee.hhh.....ee...ee.....eeeeeeeeee........eeeeeeehhhheeeeeee..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1uwe V    4 LLAQSGPELVKPGASVKISCAASAYSITDFTIYWVKQSHGDSLEWIGGIDPHNGGGAYNQKFRVKATLTVDTSSSTAYIHLNSLTSEDSAVYYCAIFYGNFFDYWGQGTTVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTAVDKAVEPKSC  216
                             |      12        22        32        42        52|       61        71        81        91      100A||     108       118       128       138       148       158       168       178       188       198       208        
                            4A                                              52A                                             100A||                                                                                                                    
                                                                                                                             100B|                                                                                                                    
                                                                                                                              100C                                                                                                                    


Chain X from PDB  Type:PROTEIN  Length:213
                                                                                                                                                                                                                                                      
               SCOP domains d1uwex1 X:1-107 Immunoglobulin light chain kappa variable domain, VL-kappa                                  d1uwex2 X:108-212 Immunoglobulin light chain kappa constant domain, CL-kappa                              SCOP domains
               CATH domains -1uweX01 X:1A-108 Immunoglobulins                                                                            1uweX02 X:109-212 Immunoglobulins                                                                        CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee..eeeee....eeeeeee.......eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee......ee...eeeeee......eeeee..hhhhhh..eeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhhhh.eeeeeee.......eeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1uwe X    1 LDNVMTQSPSFMSTSVGDRVSVTCAASQNVGTNVAWYQQKPGQPPKALIYSTSYRYSGVPDRFTGSGSGTDFTLTISNVNSEDLAEYFCQQYNIYPVTFGGGTKLEIKRTVAAPSVFIFPPSAEQLASGTASVVCLLNNFYPREAAVQWKVDNALQSGNSQESVTEQDSADSTYSLSSTLTLSKADYEAHAVYACEVTHQGLSSPVTKSFNRG  212
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209   
                            1A                                                                                                                                                                                                                   


Chain Y from PDB  Type:PROTEIN  Length:218
                                                                                                                                                                                                                                                           
               SCOP domains d1uwey1 Y:4-113 Immunoglobulin heavy chain variable domain, VH                                                     d1uwey2 Y:114-216 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                         SCOP domains
               CATH domains 1uweY01 Y:4-113 Immunoglobulins                                                                                    1uweY02 Y:114-212 Immunoglobulins                                                                  ---- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee...eee.....eeeeeee...hhhhheeeeeeee...eeeeeeee.......ee.hhhh..eeeeeehhh.eeeeee...hhhhheeeeeeeee...eeee...eeeee........eeeee..hhh.ee..eeeeeeeeeee.....eeee.hhh.....ee...ee.....eeeeeeeeee.hhhhh...eeeeee....eeeeee...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1uwe Y    4 LLAQSGPELVKPGASVKISCAASAYSITDFTIYWVKQSHGDSLEWIGGIDPHNGGGAYNQKFRVKATLTVDTSSSTAYIHLNSLTSEDSAVYYCAIFYGNFFDYWGQGTTVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTAVDKAVEPKSC  216
                             |      12        22        32        42        52|       61        71        81        91      100A||     108       118       128       138       148       158       168       178       188       198       208        
                            4A                                              52A                                             100A||                                                                                                                    
                                                                                                                             100B|                                                                                                                    
                                                                                                                              100C
   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, 12)

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

(-) CATH Domains  (1, 12)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)
(-)
Architecture: Sandwich (5577)
(-)
Topology: Immunoglobulin-like (3897)
(-)
Homologous Superfamily: Immunoglobulins (2282)
(-)
Mus musculus, homo sapiens. Organism_taxid: 10090, 9606. (1)
1a1uweL02L:109-212
1b1uweU02U:109-212
1c1uweV01V:4-113
1d1uweY01Y:4-113
1e1uweX02X:109-212
1f1uweL01L:1A-108
1g1uweU01U:1A-108
1h1uweX01X:1A-108
1i1uweH02H:114-214
1j1uweV02V:114-212
1k1uweY02Y:114-212
1l1uweH01H:4-113

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 1UWE)

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  Cis Peptide Bonds
    Glu H:148 - Pro H:149   [ RasMol ]  
    Glu V:148 - Pro V:149   [ RasMol ]  
    Glu Y:148 - Pro Y:149   [ RasMol ]  
    Phe H:146 - Pro H:147   [ RasMol ]  
    Phe V:146 - Pro V:147   [ RasMol ]  
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    Tyr L:94 - Pro L:95   [ RasMol ]  
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    Tyr U:94 - Pro U:95   [ RasMol ]  
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  1uwe
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(-) Related Entries Specified in the PDB File

1uwg MOLECULAR MECHANISM OF ENANTIOSELECTIVE PROTON TRANSFER TO CARBON IN CATALYTIC ANTIBODY 14D9