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(-) Description

Title :  CRYSTALLOGRAPHIC STRUCTURE OF THE ESTEROLYTIC AND AMIDOLYTIC 43C9 ANTIBODY
 
Authors :  M. M. Thayer, E. D. Getzoff, V. A. Roberts
Date :  10 Mar 99  (Deposition) - 18 Aug 99  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Biol. Unit 3:  E,F  (1x)
Biol. Unit 4:  G,H  (1x)
Keywords :  Immunoglobulin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. M. Thayer, E. H. Olender, A. S. Arvai, C. K. Koike, I. L. Canestrelli, J. D. Stewart, S. J. Benkovic, E. D. Getzoff, V. A. Roberts
Structural Basis For Amide Hydrolysis Catalyzed By The 43C9 Antibody.
J. Mol. Biol. V. 291 329 1999
PubMed-ID: 10438624  |  Reference-DOI: 10.1006/JMBI.1999.2960
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEIN (IMMUNOGLOBULIN (LIGHT CHAIN))
    Chains: A, C, E, G
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Cell Line: BL21(DE3)
    Expression System Taxid: 562
    Fragment: FV
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
 
Molecule 2 - PROTEIN (IMMUNOGLOBULIN (HEAVY CHAIN))
    Chains: B, D, F, H
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Cell Line: BL21(DE3)
    Expression System Taxid: 562
    Fragment: FV
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit : ABCDEFGH
Biological Unit 1 (1x): AB      
Biological Unit 2 (1x):   CD    
Biological Unit 3 (1x):     EF  
Biological Unit 4 (1x):       GH

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 43C9)

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1AUTHORHIS A:91 , ARG A:96CATALYTIC SITE IS BELIEVED TO INCLUDE: HIS 91 IN THE VARIABLE LIGHT CHAIN - NUCLEOPHILE THAT FORMS A COVALENT BOND TO THE SUBSTRATE ARG 96 IN THE VARIABLE LIGHT CHAIN - SIDE CHAIN STABILIZES NEGATIVE CHARGE FORMED IN THE TRANSITION STATES OF THE REACTION
2AC2AUTHORHIS C:91 , ARG C:96CATALYTIC SITE IS BELIEVED TO INCLUDE: HIS 91 IN THE VARIABLE LIGHT CHAIN - NUCLEOPHILE THAT FORMS A COVALENT BOND TO THE SUBSTRATE ARG 96 IN THE VARIABLE LIGHT CHAIN - SIDE CHAIN STABILIZES NEGATIVE CHARGE FORMED IN THE TRANSITION STATES OF THE REACTION
3AC3AUTHORHIS E:91 , ARG E:96CATALYTIC SITE IS BELIEVED TO INCLUDE: HIS 91 IN THE VARIABLE LIGHT CHAIN - NUCLEOPHILE THAT FORMS A COVALENT BOND TO THE SUBSTRATE ARG 96 IN THE VARIABLE LIGHT CHAIN - SIDE CHAIN STABILIZES NEGATIVE CHARGE FORMED IN THE TRANSITION STATES OF THE REACTION
4AC4AUTHORHIS G:91 , ARG G:96CATALYTIC SITE IS BELIEVED TO INCLUDE: HIS 91 IN THE VARIABLE LIGHT CHAIN - NUCLEOPHILE THAT FORMS A COVALENT BOND TO THE SUBSTRATE ARG 96 IN THE VARIABLE LIGHT CHAIN - SIDE CHAIN STABILIZES NEGATIVE CHARGE FORMED IN THE TRANSITION STATES OF THE REACTION

(-) SS Bonds  (8, 8)

Asymmetric Unit
No.Residues
1A:23 -A:88
2B:22 -B:92
3C:23 -C:88
4D:22 -D:92
5E:23 -E:88
6F:22 -F:92
7G:23 -G:88
8H:22 -H:92

(-) Cis Peptide Bonds  (8, 8)

Asymmetric Unit
No.Residues
1Thr A:7 -Pro A:8
2Ala A:94 -Pro A:95
3Thr C:7 -Pro C:8
4Ala C:94 -Pro C:95
5Thr E:7 -Pro E:8
6Ala E:94 -Pro E:95
7Thr G:7 -Pro G:8
8Ala G:94 -Pro G:95

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 43C9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 43C9)

(-) Exons   (0, 0)

(no "Exon" information available for 43C9)

(-) 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:113
                                                                                                                                                  
               SCOP domains d43c9a_ A: Immunoglobulin light chain kappa variable domain, VL-kappa                                             SCOP domains
               CATH domains 43c9A00 A:1-107 Immunoglobulins                                                                                   CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeee..............eeeeee.....eeeee.............eeeeee..eeeeee...hhhhheeeeeee...........eeeeee Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------- Transcript
                43c9 A    1 DVVMTQTPSSLAMSVGQKVTMSCKSSQSLLNISNQKNYLAWYQQKPGQSPKLLVYFASTRESGVPDRFIGSGSGTDFTLTISSVQAEDQADYFCQQHYRAPRTFGGGTKLEIK  107
                                    10        20       27C|||     34        44        54        64        74        84        94       104   
                                                     27A|||||                                                                                
                                                      27B||||                                                                                
                                                       27C|||                                                                                
                                                        27D||                                                                                
                                                         27E|                                                                                
                                                          27F                                                                                


Chain B from PDB  Type:PROTEIN  Length:118
 aligned with HVM44_MOUSE | P01820 from UniProtKB/Swiss-Prot  Length:115

    Alignment length:118
                                                                                                                          115                     
                                    28        38        48        58        68        78        88        98       108      |  -         -        
         HVM44_MOUSE     19 SQVQLKESGPGLVAPSQSLSITCTVSGFSLTGYGVNWVRQPPGKGLEWLGMIWGDGSTDYNSALKSRLSISKDNSKSQVFLKMNSLQTDDTARYYCA---------------------    -
               SCOP domains d43c9b_ B: Immunoglobulin heavy chain variable domain, VH                                                              SCOP domains
               CATH domains 43c9B00 B:0-112 Immunoglobulins                                                                                        CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee..........eeeeeeee..hhhhheeeeeeee...eeeeeeee.....eee..hhhh.eeeeee....eeeeee...hhhhheeeeeeee.......eee...eee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------- Transcript
                43c9 B    0 GQVQLVESGPGLVAPSQSLSITCTVSGISLSRYNVHWVRQSPGKGLEWLGMIWGGGSIEYNPALKSRLSISKDNSKSQIFLKMNSLQTDDSAMYYCVSYGYGGDRFSYWGQGTLVTVS  112
                                     9        19        29        39        49        59        69        79   |||  86        96    || 104        
                                                                                                             82A||               100A|            
                                                                                                              82B|                100B            
                                                                                                               82C                                


Chain C from PDB  Type:PROTEIN  Length:113
                                                                                                                                                  
               SCOP domains d43c9c_ C: Immunoglobulin light chain kappa variable domain, VL-kappa                                             SCOP domains
               CATH domains 43c9C00 C:1-107 Immunoglobulins                                                                                   CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeee..............eeeeee......eeee.............eeeeee..eeeeee...hhhhheeeeeee...........eeeeee Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------- Transcript
                43c9 C    1 DVVMTQTPSSLAMSVGQKVTMSCKSSQSLLNISNQKNYLAWYQQKPGQSPKLLVYFASTRESGVPDRFIGSGSGTDFTLTISSVQAEDQADYFCQQHYRAPRTFGGGTKLEIK  107
                                    10        20       27C|||     34        44        54        64        74        84        94       104   
                                                     27A|||||                                                                                
                                                      27B||||                                                                                
                                                       27C|||                                                                                
                                                        27D||                                                                                
                                                         27E|                                                                                
                                                          27F                                                                                


Chain D from PDB  Type:PROTEIN  Length:118
 aligned with HVM44_MOUSE | P01820 from UniProtKB/Swiss-Prot  Length:115

    Alignment length:118
                                                                                                                          115                     
                                    28        38        48        58        68        78        88        98       108      |  -         -        
         HVM44_MOUSE     19 SQVQLKESGPGLVAPSQSLSITCTVSGFSLTGYGVNWVRQPPGKGLEWLGMIWGDGSTDYNSALKSRLSISKDNSKSQVFLKMNSLQTDDTARYYCA---------------------    -
               SCOP domains d43c9d_ D: Immunoglobulin heavy chain variable domain, VH                                                              SCOP domains
               CATH domains 43c9D00 D:0-112 Immunoglobulins                                                                                        CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee..........eeeeeeee.......eeeeeeee...eeeeeeee.....eee.hhhh..eeeeeehhh.eeeeee...hhhhheeeeeeeee......eee...eee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------- Transcript
                43c9 D    0 GQVQLVESGPGLVAPSQSLSITCTVSGISLSRYNVHWVRQSPGKGLEWLGMIWGGGSIEYNPALKSRLSISKDNSKSQIFLKMNSLQTDDSAMYYCVSYGYGGDRFSYWGQGTLVTVS  112
                                     9        19        29        39        49        59        69        79   |||  86        96    || 104        
                                                                                                             82A||               100A|            
                                                                                                              82B|                100B            
                                                                                                               82C                                


Chain E from PDB  Type:PROTEIN  Length:113
                                                                                                                                                  
               SCOP domains d43c9e_ E: Immunoglobulin light chain kappa variable domain, VL-kappa                                             SCOP domains
               CATH domains 43c9E00 E:1-107 Immunoglobulins                                                                                   CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeee..............eeeeee......eeee.............eeeeee..eeeeee........eeeeeee...........eeeeee Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------- Transcript
                43c9 E    1 DVVMTQTPSSLAMSVGQKVTMSCKSSQSLLNISNQKNYLAWYQQKPGQSPKLLVYFASTRESGVPDRFIGSGSGTDFTLTISSVQAEDQADYFCQQHYRAPRTFGGGTKLEIK  107
                                    10        20       27C|||     34        44        54        64        74        84        94       104   
                                                     27A|||||                                                                                
                                                      27B||||                                                                                
                                                       27C|||                                                                                
                                                        27D||                                                                                
                                                         27E|                                                                                
                                                          27F                                                                                


Chain F from PDB  Type:PROTEIN  Length:118
 aligned with HVM44_MOUSE | P01820 from UniProtKB/Swiss-Prot  Length:115

    Alignment length:118
                                                                                                                          115                     
                                    28        38        48        58        68        78        88        98       108      |  -         -        
         HVM44_MOUSE     19 SQVQLKESGPGLVAPSQSLSITCTVSGFSLTGYGVNWVRQPPGKGLEWLGMIWGDGSTDYNSALKSRLSISKDNSKSQVFLKMNSLQTDDTARYYCA---------------------    -
               SCOP domains d43c9f_ F: Immunoglobulin heavy chain variable domain, VH                                                              SCOP domains
               CATH domains 43c9F00 F:0-112 Immunoglobulins                                                                                        CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee............eeeeee.......eeeeeeee...eeeeeeee.....eeehhhhhh...eeee....eeee.....hhhhheeeeeeee.......eee...eee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------- Transcript
                43c9 F    0 GQVQLVESGPGLVAPSQSLSITCTVSGISLSRYNVHWVRQSPGKGLEWLGMIWGGGSIEYNPALKSRLSISKDNSKSQIFLKMNSLQTDDSAMYYCVSYGYGGDRFSYWGQGTLVTVS  112
                                     9        19        29        39        49        59        69        79   |||  86        96    || 104        
                                                                                                             82A||               100A|            
                                                                                                              82B|                100B            
                                                                                                               82C                                


Chain G from PDB  Type:PROTEIN  Length:113
                                                                                                                                                  
               SCOP domains d43c9g_ G: Immunoglobulin light chain kappa variable domain, VL-kappa                                             SCOP domains
               CATH domains 43c9G00 G:1-107 Immunoglobulins                                                                                   CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeee..............eeeeee......eeee.............eeeeee..eeeeee...hhhhheeeeeee...........eeeeee Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------- Transcript
                43c9 G    1 DVVMTQTPSSLAMSVGQKVTMSCKSSQSLLNISNQKNYLAWYQQKPGQSPKLLVYFASTRESGVPDRFIGSGSGTDFTLTISSVQAEDQADYFCQQHYRAPRTFGGGTKLEIK  107
                                    10        20       27C|||     34        44        54        64        74        84        94       104   
                                                     27A|||||                                                                                
                                                      27B||||                                                                                
                                                       27C|||                                                                                
                                                        27D||                                                                                
                                                         27E|                                                                                
                                                          27F                                                                                


Chain H from PDB  Type:PROTEIN  Length:118
 aligned with HVM44_MOUSE | P01820 from UniProtKB/Swiss-Prot  Length:115

    Alignment length:118
                                                                                                                          115                     
                                    28        38        48        58        68        78        88        98       108      |  -         -        
         HVM44_MOUSE     19 SQVQLKESGPGLVAPSQSLSITCTVSGFSLTGYGVNWVRQPPGKGLEWLGMIWGDGSTDYNSALKSRLSISKDNSKSQVFLKMNSLQTDDTARYYCA---------------------    -
               SCOP domains d43c9h_ H: Immunoglobulin heavy chain variable domain, VH                                                              SCOP domains
               CATH domains 43c9H00 H:0-112 Immunoglobulins                                                                                        CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee............eeeeee.......eeeeeeee...eeeeeeee.....eeehhhhhh...eeee....eeee.....hhhhheeeeeeee.......eee...eee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------- Transcript
                43c9 H    0 GQVQLVESGPGLVAPSQSLSITCTVSGISLSRYNVHWVRQSPGKGLEWLGMIWGGGSIEYNPALKSRLSISKDNSKSQIFLKMNSLQTDDSAMYYCVSYGYGGDRFSYWGQGTLVTVS  112
                                     9        19        29        39        49        59        69        79   |||  86        96    || 104        
                                                                                                             82A||               100A|            
                                                                                                              82B|                100B            
                                                                                                               82C
   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  (2, 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)
1a43c9A00A:1-107
1b43c9C00C:1-107
1c43c9E00E:1-107
1d43c9G00G:1-107
1e43c9B00B:0-112
1f43c9D00D:0-112
1g43c9F00F:0-112
1h43c9H00H:0-112

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 43C9)

(-) Gene Ontology  (1, 1)

Asymmetric Unit(hide GO term definitions)
Chain B,D,F,H   (HVM44_MOUSE | P01820)
molecular function
    GO:0003823    antigen binding    Interacting selectively and non-covalently with an antigen, any substance which is capable of inducing a specific immune response and of reacting with the products of that response, the specific antibody or specifically sensitized T-lymphocytes, or both. Binding may counteract the biological activity of the antigen.

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  43c9
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  HVM44_MOUSE | P01820
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 Related Entries

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

UniProtKB/Swiss-Prot
        HVM44_MOUSE | P01820: 1a2y 1a7n 1a7o 1a7p 1a7q 1a7r 1dl7 1dvf 1g7h 1g7i 1g7j 1g7l 1g7m 1kir 1p4b 1p4i 1vfa 1vfb 43ca

(-) Related Entries Specified in the PDB File

43ca