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(-) Description

Title :  CRYSTAL STRUCTURE OF THE FAB FRAGMENT OF ESTEROLYTIC ANTIBODY MS5-393
 
Authors :  S. N. Ruzheinikov, T. A. Muranova, S. E. Sedelnikova, L. J. Partridge, G. M. Blackburn, I. A. Murray, H. Kakinuma, N. Takashi, K. Shimazaki, J Y. Nishi, D. W. Rice
Date :  23 Aug 02  (Deposition) - 23 Sep 03  (Release) - 16 Nov 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym./Biol. Unit :  H,L
Keywords :  Catalytic Antibody, Ester Hydrolysis, Esterolytic, Fab, Immunoglobulin, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. N. Ruzheinikov, T. A. Muranova, S. E. Sedelnikova, L. J. Partridge, G. M. Blackburn, I. A. Murray, H. Kakinuma, N. Takashi, K. Shimazaki, J. Sun, Y. Nishi, D. W. Rice
High-Resolution Crystal Structure Of The Fab-Fragments Of A Family Of Mouse Catalytic Antibodies With Esterase Activity
J. Mol. Biol. V. 332 423 2003
PubMed-ID: 12948492  |  Reference-DOI: 10.1016/S0022-2836(03)00902-1
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - IMMUNOGLOBULIN MS5-393
    Cell Line: HYBRIDOMA
    Chains: L
    Engineered: YES
    Expression System: MUS MUSCULUS
    Expression System Common: HOUSE MOUSE
    Expression System Taxid: 10090
    Fragment: FAB FRAGMENT, LIGHT CHAIN
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Other Details: FUSING OF MOUSE SPLENOCYTES WITH MYELOMA CELL
 
Molecule 2 - IMMUNOGLOBULIN MS5-393
    Cell Line: HYBRIDOMA
    Chains: H
    Engineered: YES
    Expression System: MUS MUSCULUS
    Expression System Common: HOUSE MOUSE
    Expression System Taxid: 10090
    Fragment: FAB FRAGMENT, HEAVY CHAIN
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Other Details: FUSING OF MOUSE SPLENOCYTES WITH MYELOMA CELL

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : HL

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 1MIE)

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1H:22 -H:92
2H:142 -H:208
3L:23 -L:88
4L:134 -L:194

(-) Cis Peptide Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1Tyr L:94 -Pro L:95
2Tyr L:140 -Pro L:141
3Phe H:148 -Pro H:149
4Glu H:150 -Pro H:151
5Trp H:199 -Pro H:200

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1MIE)

(-) Sequences/Alignments

Asymmetric/Biological 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:191
                                                                                                                                                                                                                               
               SCOP domains d1mieh1 H:5-113 Immunoglobulin heavy chain variable domain, VH                                   d1mieh2 H:114-228 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                SCOP domains
               CATH domains 1mieH01 H:5-113 Immunoglobulins                                                                  1mieH02 H:114-223 Immunoglobulins                                                          --- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee.......eeee...eeeee......ee.............hhhhhh.ee..........eeee........eeeeee.......eee..........eeeee....eeeeeeeeeee.....eeee.hhh....eeeeeeeee..eeeeeeeeeee.hhh.....eeeeeehhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1mie H   5 QQPGAELVKPGASVKLSCWINWVKQRPGQGLEWIGNVYPGSSSTNYNEKFKNKATLTVDTSSSTAYMQLSSLTSDDSAFYYCVRPYWGQGTLVTVSAAKTTAPSVYPLAPVSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIEPR 228
                                    14       |34        44        53        63        73       82A||      90   ||  106       116       126||     144       154|||    169|      180|      192   || |204 ||    215       227 
                                            22|                 52A                            82A||          94|                       127|               154|||    169|      180|          196| || 206|            223|  
                                             33                                                 82B|          101                        136                157||     171       183           198 ||  208             226  
                                                                                                 82C                                                         158|                               200|                       
                                                                                                                                                              162                                202                       


Chain L from PDB  Type:PROTEIN  Length:218
                                                                                                                                                                                                                                                          
               SCOP domains d1miel1 L:1-107 Immunoglobulin light chain kappa variable domain, VL-kappa                                      d1miel2 L:108-213 Immunoglobulin light chain kappa constant domain, CL-kappa                               SCOP domains
               CATH domains 1mieL01 L:1-108 Immunoglobulins                                                                                  1mieL02 L:109-211 Immunoglobulins                                                                      -- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee....eeee.....eeeeeee............eeeeee......eeeee...ee.......eeeee...eeeeee...hhhhheeeeeee......ee...eeeee.......eeeee..hhhhhhh.eeeeeeeeeee....eeeeeee..eee...eeeee.........eeeeeeeeeehhhhh...eeeeeeee......eeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1mie L   1 EIVMTQAAPSVPVTPGESVSISCRSSKSLLHSNGNTYLNWFLQRPGQSPQLLIYRMSNLASGVPDRFSGSGSETAFTLRTSRVEAEDVGVYYCMQHLEYPFTFGSGTKLELKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNE 213
                                    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)
  - → Gap (green background, '-', border residues have a numbering label)
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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/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
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  Sites
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  Cis Peptide Bonds
    Glu H:150 - Pro H:151   [ RasMol ]  
    Phe H:148 - Pro H:149   [ RasMol ]  
    Trp H:199 - Pro H:200   [ RasMol ]  
    Tyr L:140 - Pro L:141   [ RasMol ]  
    Tyr L:94 - Pro L:95   [ RasMol ]  
 

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 Related Entries

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

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(-) Related Entries Specified in the PDB File

1mh5 THE STRUCTURE OF THE COMPLEX OF THE FAB FRAGMENT OF THEESTEROLYTIC ANTIBODY MS6-164 AND A TRANSITION-STATE ANALOG
1mj7 CRYSTAL STRUCTURE OF THE COMPLEX OF THE FAB FRAGMENT OF ESTEROLYTIC ANTIBODY MS5-393D9 AND A TRANSITION-STATE ANALOG
1mj8 HIGH RESOLUTION CRYSTAL STRUCTURE OF THE COMPLEX OF THE FAB FRAGMENT OF THE ESTEROLYTIC ANTIBODY MS6-126 AND A TRANSITION-STATE ANALOG
1mjj HIGH RESOLUTION CRYSTAL STRUCTURE OF THE COMPLEX OF THE FAB FRAGMENT OF ESTEROLYTIC ANTIBODY MS6-12 AND A TRANSITION- STATE ANALOG
1mju 1.22 ANGSTROM RESOLUTION CRYSTAL STRUCTURE OF THE COMPLEX OF THE FAB FRAGMENT OF ESTEROLYTIC ANTIBODY MS6-12