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(-) Description

Title :  PREPARATION, CHARACTERIZATION AND CRYSTALLIZATION OF AN ANTIBODY FAB FRAGMENT THAT RECOGNIZES RNA. CRYSTAL STRUCTURES OF NATIVE FAB AND THREE FAB-MONONUCLEOTIDE COMPLEXES
 
Authors :  P. R. Pokkuluri, M. Cygler
Date :  13 Jun 94  (Deposition) - 14 Feb 95  (Release) - 25 Aug 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  H,L
Keywords :  Immunoglobulin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. R. Pokkuluri, F. Bouthillier, Y. Li, A. Kuderova, J. Lee, M. Cygler
Preparation, Characterization And Crystallization Of An Antibody Fab Fragment That Recognizes Rna. Crystal Structures Of Native Fab And Three Fab-Mononucleotide Complexes.
J. Mol. Biol. V. 243 283 1994
PubMed-ID: 7523684  |  Reference-DOI: 10.1006/JMBI.1994.1654
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - IGG2B-KAPPA JEL103 FAB (LIGHT CHAIN)
    Chains: L
    Engineered: YES
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
 
Molecule 2 - IGG2B-KAPPA JEL103 FAB (HEAVY CHAIN)
    Chains: H
    Engineered: YES
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : HL

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 3)

Asymmetric/Biological Unit (3, 3)
No.NameCountTypeFull Name
1IDP1Ligand/IonINOSINE-5'-DIPHOSPHATE
2IMD1Ligand/IonIMIDAZOLE
3ZN1Ligand/IonZINC ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP H:220 , ASP L:151 , HIS L:189 , IMD L:902BINDING SITE FOR RESIDUE ZN L 600
2AC2SOFTWARESER H:163 , SER H:209 , THR H:218 , ASP H:220 , ASP L:151 , ARG L:188 , HIS L:189 , ZN L:600BINDING SITE FOR RESIDUE IMD L 902
3AC3SOFTWAREARG H:96 , HOH H:685 , ASN L:28 , ASN L:30 , TYR L:32 , LYS L:50 , GLU L:79 , GLU L:81 , SER L:91 , LYS L:169 , HOH L:690BINDING SITE FOR RESIDUE IDP L 901

(-) 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
1Thr L:7 -Pro L:8
2Val L:94 -Pro L:95
3Tyr L:140 -Pro L:141
4Phe H:148 -Pro H:149
5Trp H:199 -Pro H:200

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1MRD)

(-) 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:208
                                                                                                                                                                                                                                                
               SCOP domains d1mrdh1 H:2-115 Immunoglobulin heavy chain variable domain, VH                                                    d1mrdh2 H:116-227 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                SCOP domains
               CATH domains 1mrdH01 H:2-113 Immunoglobulins                                                                                 1mrdH02 H:114-223 Immunoglobulins                                                             -- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeee.eeeeeeeeee......eeeeeeeee....eeeeeeee...eeeeeehhhh..eeeeee.eeeeeee..hhhhheeeeeee......eeeeeeeeeee.......eeeee.......eeeeeeeeee......eeeeehhh....eeeeeeeee..eeeeeeeeeee.hhh....eeeeeeehhhheeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1mrd H   2 VQLQQSGAELVKPGASVKLSCKASGYTFTSYWMQWVKQRPGQGLEWIGEIDPSDSYTNYNQKFKGKATLTVDSTAYMQLSSLTSEDSAVYYCANLRGYFDYWGQGTTLTVSSAKTTPPSVYPLAPGTTGSSVTLGCLVKGYFPESVTVTWNSGSLSSSVHTFPALLQSGLYTMSSSVTVPSSTWPSQTVTCSVAHPASSTTVDKKLEP 227
                                    11        21        31        41        51 |      60        70 ||    82A||      90       101       111       121     ||136       146       157|      172       184       194 || || 206|      217     || 
                                                                             52A                  72|    82A||               99|                       127|                  154|||    169|      180|          196| || 206|            223| 
                                                                                                   76     82B|               101                        133                   156||     171       183           198 ||  208             226 
                                                                                                           82C                                                                 157|                               200|                      
                                                                                                                                                                                162                                202                      


Chain L from PDB  Type:PROTEIN  Length:216
                                                                                                                                                                                                                                                        
               SCOP domains d1mrdl1 L:1-108 Immunoglobulin light chain kappa variable domain, VL-kappa                                       d1mrdl2 L:109-211 Immunoglobulin light chain kappa constant domain, CL-kappa                            SCOP domains
               CATH domains 1mrdL01 L:1-107 Immunoglobulins                                                                                 1mrdL02 L:108-211 Immunoglobulins                                                                        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
     Sec.struct. author (1) .eeeeee..eeee...eeeeeeeee...........eeeeeee...eeeeeeeee..eeee.....eeeeee..eeeeee...hhhhheeeeeeee.....eeeeeeeeeee......-------hhhhhhh.eeeeeeeeeeee..eeeeeeeee.......eeeeeeeee....eeeeeeeeeeehhhhhhheeeeeeeee....eeeeeeeee Sec.struct. author (1)
     Sec.struct. author (2) ----------------------------------------------------------------------------------------------------------------------eeeeeeee------------------------------------------------------------------------------------------ Sec.struct. author (2)
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1mrd L   1 DVVMTQTPLSLPVSLGDQASISCRSSQSLVHSNGNTYLHWYLQKPGQSPKLLIYKVSNRFSGVPDRFSGSGSGTDFTLKISRVEAEDLGVYFCSQSTHVPRTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGKERQNGVLNSWTDQNSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR 211
                                    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
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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 1MRD)

(-) Gene Ontology  (0, 0)

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

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    Val L:94 - Pro L:95   [ RasMol ]  
 

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