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(-) Description

Title :  HIGH RESOLUTION CRYSTAL STRUCTURE OF THE FAB FRAGMENT OF THE ESTEROLYTIC ANTIBODY MS6-126
 
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 :  27 Aug 02  (Deposition) - 23 Sep 03  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.75
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 MS6-126
    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 MS6-126
    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  (2, 7)

Asymmetric/Biological Unit (2, 7)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2PO45Ligand/IonPHOSPHATE ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU H:61 , ARG H:62 , GLU L:1 , PRO L:95 , HOH L:885 , HOH L:1055BINDING SITE FOR RESIDUE PO4 L 801
2AC2SOFTWAREALA L:8 , SER L:22 , HOH L:993 , HOH L:994BINDING SITE FOR RESIDUE PO4 L 802
3AC3SOFTWAREHIS H:172 , HOH H:829 , THR L:164 , ASP L:165 , ASP L:167 , HOH L:932 , HOH L:935 , HOH L:964BINDING SITE FOR RESIDUE PO4 L 803
4AC4SOFTWARESER H:65 , LYS H:66 , SER H:82A , SER H:82B , TYR H:102 , HOH H:1029 , HOH H:1047BINDING SITE FOR RESIDUE PO4 H 804
5AC5SOFTWARETRP H:33 , ASN H:35 , ASN H:50 , LYS H:95 , GOL H:701 , HOH H:863 , HIS L:91 , PHE L:96BINDING SITE FOR RESIDUE PO4 H 805
6AC6SOFTWAREPHE H:174 , PRO H:175 , THR H:186 , LEU H:187 , SER H:188 , HOH H:827 , HOH H:831 , SER L:176 , THR L:178BINDING SITE FOR RESIDUE GOL H 700
7AC7SOFTWAREASN H:35 , LYS H:95 , PO4 H:805BINDING SITE FOR RESIDUE GOL H 701

(-) SS Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1H:22 -H:92
2H:142 -H:208
3L:23 -L:88
4L:134 -L:194
5L:214 -H:128

(-) 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 1MJ8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1MJ8)

(-) Exons   (0, 0)

(no "Exon" information available for 1MJ8)

(-) 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:216
                                                                                                                                                                                                                                                         
               SCOP domains d1mj8h1 H:2-113 Immunoglobulin heavy chain variable domain, VH                                                        d1mj8h2 H:114-231 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                    SCOP domains
               CATH domains 1mj8H01 H:2-113 Immunoglobulins                                                                                       1mj8H02 H:114-227 Immunoglobulins                                                             ---- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..ee...eeee.....eeeeeee...hhhhh.eeeeee......eeeeee......eee.hhhh..eeeeeehhh.eeeeee...hhhhheeeeeeee.......eee...eeeee........eeeee.....eeeeeeeeeee.....eeee.hhh....eee...eee..eeeeeeeeeee.........eeeeeehhhheeeeee....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                1mj8 H    2 VQLQQPGAELVKPGASVKLSCKASGYTFTSNWINWVKQRPGQGLEWIGNIYPGSGYTNYNERFKSKATLTVDTSSSTAYMQLSSLTSDDSAVYYCARKHYFYDGVVYWGQGTLVTVSAAKTTAPSVYPLAPVCSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIEPRGPT  231
                                    11        21        31        41        51 |      60        70        80  |||   87        97   ||  105       115       125  ||   142       152 ||||  167 ||    178 ||    190     ||202   ||  213       223|     
                                                                             52A                            82A||               100A|                         128|               154|||    169|      180|          196| || 206|            223|     
                                                                                                             82B|                100B                          136                157||     171       183           198 ||  208             226     
                                                                                                              82C                                                                  158|                               200|                          
                                                                                                                                                                                    162                                202                          


Chain L from PDB  Type:PROTEIN  Length:214
                                                                                                                                                                                                                                                       
               SCOP domains d1mj8l1 L:1-107 Immunoglobulin light chain kappa variable domain, VL-kappa                                      d1mj8l2 L:108-214 Immunoglobulin light chain kappa constant domain, CL-kappa                           SCOP domains
               CATH domains 1mj8L01 L:1-108 Immunoglobulins                                                                                  1mj8L02 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..hhhhhh..eeeeeeeeeee.....eeeeee..eee...eeeee.........eeeeeeeeeehhhhhh..eeeeeee..eeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1mj8 L    1 EIVMTQAAPSVPVTPGESVSISCRSSKSLLHSNGNTYLYWFLQRPGQSPQLLIYRMSNLASGVPDRFSGSGSGTAFTLRISRVEAEDVGVYYCLQHLEYPFTFGAGTKLELKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHPIVKSFNRNEC  214
                                    10        20       27C||      35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195  ||   210    
                                                     27A||||                                                                                                                                                                        198|          
                                                      27B|||                                                                                                                                                                         204          
                                                       27C||                                                                                                                                                                                      
                                                        27D|                                                                                                                                                                                      
                                                         27E
   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, 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 1MJ8)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 1MJ8)

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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

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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
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1mj7 CRYSTAL STRUCTURE OF THE COMPLEX OF THE FAB FRAGMENT OF ESTEROLYTIC ANTIBODY MS5-393D9 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