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(-) Description

Title :  THREE DIMENSIONAL STRUCTURE OF THE FAB FRAGMENT OF A NEUTRALIZING ANTIBODY TO HUMAN RHINOVIRUS SEROTYPE 2
 
Authors :  J. Tormo, D. Blaas, I. Fita
Date :  05 May 92  (Deposition) - 31 Jan 94  (Release) - 05 Feb 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym./Biol. Unit :  H,L
Keywords :  Immunoglobulin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Tormo, E. Stadler, T. Skern, H. Auer, O. Kanzler, C. Betzel, D. Blaas I. Fita
Three-Dimensional Structure Of The Fab Fragment Of A Neutralizing Antibody To Human Rhinovirus Serotype 2.
Protein Sci. V. 1 1154 1992
PubMed-ID: 1338980
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - IGG2A-KAPPA 8F5 FAB (LIGHT CHAIN)
    Chains: L
    Engineered: YES
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
 
Molecule 2 - IGG2A-KAPPA 8F5 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  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1SO41Ligand/IonSULFATE ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR H:33 , HIS H:35 , ARG H:50 , HOH H:721BINDING SITE FOR RESIDUE SO4 H 720
2H1UNKNOWNASP H:31 , ILE H:32 , TYR H:33 , ILE H:34 , HIS H:35NULL
3H2UNKNOWNARG H:50 , LEU H:51 , ASP H:52 , PRO H:53 , ALA H:54 , ASN H:55 , GLY H:56 , TYR H:57 , THR H:58 , LYS H:59 , TYR H:60 , ASP H:61 , PRO H:62 , LYS H:63 , PHE H:64 , GLN H:65 , GLY H:66NULL
4H3UNKNOWNTYR H:99 , TYR H:100 , SER H:101 , TYR H:102 , TYR H:103 , ASP H:104 , MET H:105 , ASP H:106 , TYR H:107NULL
5L1UNKNOWNLYS L:24 , SER L:25 , SER L:26 , GLN L:27 , SER L:28 , LEU L:29 , LEU L:30 , ASN L:31 , SER L:32 , ARG L:33 , THR L:34 , GLN L:35 , LYS L:36 , ASN L:37 , TYR L:38 , LEU L:39 , THR L:40NULL
6L2UNKNOWNPRO L:50 , LYS L:51 , LEU L:52 , LEU L:53 , ILE L:54 , TYR L:55 , TRP L:56 , ALA L:57 , SER L:58 , THR L:59 , ARG L:60 , GLU L:61 , SER L:62NULL
7L3UNKNOWNLEU L:89 , ALA L:90 , VAL L:91 , TYR L:92 , TYR L:93 , CYS L:94 , GLN L:95 , ASN L:96 , ASN L:97 , TYR L:98 , ASN L:99 , TYR L:100 , PRO L:101 , LEU L:102 , THR L:103NULL

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1H:22 -H:96
2H:145 -H:200
3L:23 -L:94
4L:140 -L:200

(-) Cis Peptide Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1Ser L:7 -Pro L:8
2Tyr L:100 -Pro L:101
3Tyr L:146 -Pro L:147
4Phe H:151 -Pro H:152
5Glu H:153 -Pro H:154
6Trp H:193 -Pro H:194

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1BBD)

(-) 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:213
                                                                                                                                                                                                                                                     
               SCOP domains d1bbdh1 H:1-119 Immunoglobulin heavy chain variable domain, VH                                                         d1bbdh2 H:120-218 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                SCOP domains
               CATH domains 1bbdH01 H:1-118 Immunoglobulins                                                                                       1bbdH02 H:119-215 Immunoglobulins                                                           --- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee.......eeeeeee.....eeeeeeee....eeee.......eeeeee....eeeeee........eeeeeeee......eee...eeeee........eeeee.....eeeeeeeeeee.....eeee........eee...ee....eeeeeeeeeehhh......eeeeee....eeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1bbd H   1 EVQLQQSGAELVRPGASVKLSCTTSGFNIKDIYIHWVKQRPEQGLEWIGRLDPANGYTKYDPKFQGKATITVDTSSNTAYLHLSSLTSEDTAVYYCDGYYSYYDMDYWGPGTSVTVSSAKTTAPSVYPLAPVCSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIEPR 218
                                    10        20        30        40        50        60        70        80        90       100       110       120       130  ||   145       155       165       175       185       195       205       215   
                                                                                                                                                              133|                                                                               
                                                                                                                                                               139                                                                               


Chain L from PDB  Type:PROTEIN  Length:219
 aligned with Q52L64_MOUSE | Q52L64 from UniProtKB/TrEMBL  Length:240

    Alignment length:219
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230         
         Q52L64_MOUSE    21 DIVMSQSPSSLAVSVGEKVTMSCKSSQSLLYSYNQKNYLAWYQQKPGQSPKLLIYWASTRESGVPDHFSGSGSGTDFTLTISSVKAEDLALYYCQQYYNYPLTFGAGTKLDLRRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNE 239
               SCOP domains d1bbdl1 L:1-114 Immunoglobulin light chain kappa variable domain, VL-kappa                                        d1bbdl2 L:115-219 Immunoglobulin light chain kappa constant domain, CL-kappa                              SCOP domains
               CATH domains 1bbdL01 L:1-114 Immunoglobulins                                                                                   1bbdL02 L:115-217 Immunoglobulins                                                                      -- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee..eeeee...eeeeeee.....ee....ee.eeeeee......eeeee...ee........eeeee..eeeeeee.......eeeeeee...........eeeeee......eeeee...hhhhhh.eeeeeeeeeee.....eeeeee..eee...ee............eeeeeeeeeehhhhhh..eeeeeee.......eeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1bbd L   1 DIVMTQSPSSLTVTTGEKVTMTCKSSQSLLNSRTQKNYLTWYQQKPGQSPKLLIYWASTRESGVPDRFTGSGSGTDFTLSISGVQAEDLAVYYCQNNYNYPLTFGAGTKLELKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNE 219
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210
   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 1BBD)

(-) Gene Ontology  (1, 1)

Asymmetric/Biological Unit(hide GO term definitions)
Chain L   (Q52L64_MOUSE | Q52L64)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.

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 Related Entries

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UniProtKB/TrEMBL
        Q52L64_MOUSE | Q52L64: 1a3r 1h3p 1jgu 1jgv 1q9w 2fd6 2r1w 2r1x 2r1y 2r23 2r2b 2r2h 3t77

(-) Related Entries Specified in the PDB File

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