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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 :  2.79
Chains :  Asym. Unit :  H,L,X,Y
Biol. Unit 1:  H,L  (1x)
Biol. Unit 2:  X,Y  (1x)
Keywords :  Antibody, Catalytic Antibody (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Zheng, U. Baumannn, 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, Y
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: TOP10
    Expression System Taxid: 562
    Expression System Vector: PBAD
    Fragment: FAB HEAVY CHAIN, RESIDUES 1-221
    Organism Common: MOUSE, HUMAN
    Organism Scientific: MUS MUSCULUS, HOMO SAPIENS
    Organism Taxid: 10090, 9606
    Other Details: CATALYTIC ANTIBODY 19C9
 
Molecule 2 - ANTIBODY 14D9
    Chains: L, X
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: TOP10
    Expression System Taxid: 562
    Expression System Vector: PBAD
    Fragment: FAB LIGHT CHAIN, RESIDUES 1-213
    Organism Common: MOUSE, HUMAN
    Organism Scientific: MUS MUSCULUS, HOMO SAPIENS
    Organism Taxid: 10090, 9606
    Other Details: CATALYTIC ANTIBODY 19C9

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : HLXY
Biological Unit 1 (1x): HL  
Biological Unit 2 (1x):   XY

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 8)
No.NameCountTypeFull Name
1KHA2Ligand/Ion1-(4-{[(2-HYDROXYETHYL)AMINO]CARBONYL}BENZYL)-1-METHYLPIPERIDINIUM
2PO46Ligand/IonPHOSPHATE ION
Biological Unit 1 (2, 6)
No.NameCountTypeFull Name
1KHA1Ligand/Ion1-(4-{[(2-HYDROXYETHYL)AMINO]CARBONYL}BENZYL)-1-METHYLPIPERIDINIUM
2PO45Ligand/IonPHOSPHATE ION
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1KHA1Ligand/Ion1-(4-{[(2-HYDROXYETHYL)AMINO]CARBONYL}BENZYL)-1-METHYLPIPERIDINIUM
2PO41Ligand/IonPHOSPHATE ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE H:51 , PRO H:57 , THR H:70 , VAL H:71BINDING SITE FOR RESIDUE PO4 H 1216
2AC2SOFTWAREGLN L:27 , ASN L:28 , HOH L:2022 , HOH L:2023BINDING SITE FOR RESIDUE PO4 L 1214
3AC3SOFTWAREGLY L:30 , THR L:31 , HIS L:32 , LYS L:183 , ALA L:184BINDING SITE FOR RESIDUE PO4 L 1215
4AC4SOFTWARETHR H:183 , SER L:114 , PHE L:116 , ASN L:137BINDING SITE FOR RESIDUE PO4 L 1216
5AC5SOFTWARELYS L:9 , PHE L:10 , LYS X:107BINDING SITE FOR RESIDUE PO4 L 1217
6AC6SOFTWARELYS L:107 , LYS X:9 , PHE X:10BINDING SITE FOR RESIDUE PO4 X 1214
7AC7SOFTWAREASN H:33 , TYR H:35 , TRP H:47 , ILE H:51 , ASP H:52 , PHE H:98 , ASP H:101 , TYR L:55 , PHE L:94BINDING SITE FOR RESIDUE KHA H 1215
8AC8SOFTWARETYR X:55 , GLN X:89 , PHE X:94 , ASN Y:33 , TYR Y:35 , TRP Y:47 , ASP Y:52 , PHE Y:98 , ASP Y:101 , HOH Y:2022BINDING SITE FOR RESIDUE KHA Y 1215

(-) SS Bonds  (8, 8)

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

(-) Cis Peptide Bonds  (10, 10)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1UWG)

(-) 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:209
                                                                                                                                                                                                                                                  
               SCOP domains d1uwgh1 H:3-113 Immunoglobulin heavy chain variable domain, VH                                                     d1uwgh2 H:114-215 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                SCOP domains
               CATH domains 1uwgH01 H:3-113 Immunoglobulins                                                                                    1uwgH02 H:114-215 Immunoglobulins                                                              CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee...eee.....eeeeeee...hhhhheeeeeee.....eeeeeee......eee.hhhh..eeeeee....eeeeee...hhhhheeeeeeee.....eee...eeeee........eeeee...eeeeeeeeee.....eeee.hhh.....ee...ee.....eeeeeeeeehhhhhhh..eeeeeeehhhheeeeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1uwg H    3 QLLESGPELVEPGASVKVSCKASAYSITDFNIYWVKQSHGKNLEWIGGIDPHNGGPVYNQKFNGKATLTVDKSSSTAFMHLNSLTSEDSAVYYCAIFYGNFFDYWGPGTTVTVSSASTKGPSVFPLAPTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKS  215
                                    12        22        32        42        52|       61        71        81        91      100A||     108       118       136       146       156       166       176       186       196       206         
                                                                            52A                                             100A||                       126|                                                                                
                                                                                                                             100B|                        135                                                                                
                                                                                                                              100C                                                                                                           


Chain L from PDB  Type:PROTEIN  Length:213
                                                                                                                                                                                                                                                      
               SCOP domains d1uwgl1 L:1-107 Immunoglobulin light chain kappa variable domain, VL-kappa                                 d1uwgl2 L:108-213 Immunoglobulin light chain kappa constant domain, CL-kappa                               SCOP domains
               CATH domains 1uwgL01 L:1-108 Immunoglobulins                                                                             1uwgL02 L:109-213 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
                1uwg L    1 ELVMTQSPKFMSTSVGDRVSVTCKASQNVGTHVAWYQQKPGQSPKTLIYSASYRYSGVPDRFTGSGSGTDFTLTIRDVQSEDAAEYFCQQYNLFPVTFGGGTKLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAAVAWKVDNALQSGNSQESVTEQDSADSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGE  213
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210   


Chain X from PDB  Type:PROTEIN  Length:213
                                                                                                                                                                                                                                                      
               SCOP domains d1uwgx1 X:1-107 Immunoglobulin light chain kappa variable domain, VL-kappa                                 d1uwgx2 X:108-213 Immunoglobulin light chain kappa constant domain, CL-kappa                               SCOP domains
               CATH domains 1uwgX01 X:1-108 Immunoglobulins                                                                             1uwgX02 X:109-213 Immunoglobulins                                                                         CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee....................................eeeeee..eeeeee...hhhhheeeeeee...........eeeee.......eeeee..........eeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhhhh.eeeeeee.......eeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1uwg X    1 ELVMTQSPKFMSTSVGDRVSVTCKASQNVGTHVAWYQQKPGQSPKTLIYSASYRYSGVPDRFTGSGSGTDFTLTIRDVQSEDAAEYFCQQYNLFPVTFGGGTKLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAAVAWKVDNALQSGNSQESVTEQDSADSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGE  213
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210   


Chain Y from PDB  Type:PROTEIN  Length:209
                                                                                                                                                                                                                                                  
               SCOP domains d1uwgy1 Y:3-113 Immunoglobulin heavy chain variable domain, VH                                                     d1uwgy2 Y:114-215 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                SCOP domains
               CATH domains 1uwgY01 Y:3-113 Immunoglobulins                                                                                    1uwgY02 Y:114-215 Immunoglobulins                                                              CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee...eee.....eeeeeee...hhhhheeeeeee.....eeeeeee......eee.hhhh..eeeeee....eeeeee...hhhhh.eeeeeeee...eeee.....eee........eeeee...eeeeeeeeee.....eeee.hhh.....ee...ee.....eeeeeeeeehhhhhhh...eeeeeehhhheeeeee..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1uwg Y    3 QLLESGPELVEPGASVKVSCKASAYSITDFNIYWVKQSHGKNLEWIGGIDPHNGGPVYNQKFNGKATLTVDKSSSTAFMHLNSLTSEDSAVYYCAIFYGNFFDYWGPGTTVTVSSASTKGPSVFPLAPTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKS  215
                                    12        22        32        42        52|       61        71        81        91      100A||     108       118       136       146       156       166       176       186       196       206         
                                                                            52A                                             100A||                       126|                                                                                
                                                                                                                             100B|                        135                                                                                
                                                                                                                              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, 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)
(-)
Mouse, human (Mus musculus, homo sapiens) (6)
1a1uwgL02L:109-213
1b1uwgX02X:109-213
1c1uwgL01L:1-108
1d1uwgX01X:1-108
1e1uwgH02H:114-215
1f1uwgY02Y:114-215
1g1uwgH01H:3-113
1h1uwgY01Y:3-113

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

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

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