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(-) Description

Title :  REFINED CRYSTAL STRUCTURE OF THE GALACTAN-BINDING IMMUNOGLOBULIN FAB J539 AT 1.95-ANGSTROMS RESOLUTION
 
Authors :  T. N. Bhat, E. A. Padlan, D. R. Davies
Date :  18 Aug 89  (Deposition) - 15 Jul 90  (Release) - 11 Sep 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym./Biol. Unit :  H,L
Keywords :  Immunoglobulin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. N. Bhat, E. A. Padlan, D. R. Davies
Refined Crystal Structure Of The Galactan-Binding Immunoglobulin Fab J539 At 1. 95-Angstroms Resolution
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - IGA-KAPPA J539 FAB (LIGHT CHAIN)
    Chains: L
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
 
Molecule 2 - IGA-KAPPA J539 FAB (HEAVY CHAIN)
    Chains: H
    Organism Common: 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, 6)

Asymmetric/Biological Unit (3, 6)
No.NameCountTypeFull Name
1FUC1Ligand/IonALPHA-L-FUCOSE
2NAG4Ligand/IonN-ACETYL-D-GLUCOSAMINE
3ZN1Ligand/IonZINC ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR H:57 , ASN H:59 , TYR H:60 , VAL H:192 , NAG H:222 , HOH H:365 , HOH H:383 , HOH H:384 , TYR L:92 , PRO L:93 , HOH L:357BINDING SITE FOR RESIDUE NAG H 221
2AC2SOFTWAREGLU H:193 , NAG H:221BINDING SITE FOR RESIDUE NAG H 222
3AC3SOFTWAREASN H:156 , THR H:158 , SER H:203 , VAL H:211 , FUC H:224 , NAG H:225BINDING SITE FOR RESIDUE NAG H 223
4AC4SOFTWARENAG H:223 , NAG H:225BINDING SITE FOR RESIDUE FUC H 224
5AC5SOFTWARETHR H:158 , NAG H:223 , FUC H:224 , HOH H:255BINDING SITE FOR RESIDUE NAG H 225
6AC6SOFTWAREGLU H:196BINDING SITE FOR RESIDUE ZN H 226

(-) SS Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1H:22 -H:96
2H:144 -H:202
3H:194 -H:218
4L:23 -L:87
5L:133 -L:193

(-) Cis Peptide Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1Ser L:7 -Pro L:8
2Tyr L:92 -Pro L:93
3Tyr L:139 -Pro L:140
4Asp H:138 -Pro H:139
5Phe H:150 -Pro H:151

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2FBJ)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2FBJ)

(-) Exons   (0, 0)

(no "Exon" information available for 2FBJ)

(-) 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:220
 aligned with HVM40_MOUSE | P01810 from UniProtKB/Swiss-Prot  Length:119

    Alignment length:220
                                                                                                                                                119                                                                                                     
                                    10        20        30        40        50        60        70        80        90       100       110        |-         -         -         -         -         -         -         -         -         -         -
          HVM40_MOUSE     1 EVKLLESGGGLVQPGGSLKLSCAASGFDFSKYWMSWVRQAPGKGLEWIGEIHPDSGTINYTPSLKDKFIISRDNAKNSLYLQMSKVRSEDTALYYCARLHYYGYNAYWGQGTLVTVSAE-----------------------------------------------------------------------------------------------------   -
               SCOP domains d2fbjh1 H:1-118 Immunoglobulin heavy chain variable domain, VH                                                        d2fbjh2 H:119-220 Immunoglobulin heavy chain alpha constant domain 1, CH1-alpha                        SCOP domains
               CATH domains 2fbjH01 H:1-118 Immunoglobulins                                                                                       2fbjH02 H:119-191 Immunoglobulins                                        ----------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..eee.....eeeeeeee..hhhhh.eeeeee.....eeeeeee......eee.......eeeee.....eeeeee...hhhhheeeeeeeee...eeeee...eeeee........eeeee..........eeeeeeeeee.....eeeee.......eeee...ee.....eeeeeeeeehhhhh....eeeeeeee.....eeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2fbj H   1 EVKLLESGGGLVQPGGSLKLSCAASGFDFSKYWMSWVRQAPGKGLEWIGEIHPDSGTINYTPSLKDKFIISRDNAKNSLYLQMSKVRSEDTALYYCARLHYYGYNAYWGQGTLVTVSAESARNPTIYPLTLPPALSSDPVIIGCLIHDYFPSGTMNVTWGKSGKDITTVNFPPALASGGRYTMSNQLTLPAVECPEGESVKCSVQHDSNPVQELDVNCSG 220
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220


Chain L from PDB  Type:PROTEIN  Length:213
 aligned with KV6A5_MOUSE | P01679 from UniProtKB/Swiss-Prot  Length:107

    Alignment length:213
                                                                                                                                    107                                                                                                          
                                    10        20        30        40        50        60        70        80        90       100      |  -         -         -         -         -         -         -         -         -         -         -   
          KV6A5_MOUSE     1 EIVLTQSPAITAASLGQKVTITCSASSSVSSLHWYQQKSGTSPKPWIYEISKLASGVPARFSGSGSGTSYSLTINTMEAEDAAIYYCQQWTYPLITFGAGTKLELKR----------------------------------------------------------------------------------------------------------   -
               SCOP domains d2fbjl1 L:1-109 Immunoglobulin light chain kappa variable domain, VL-kappa                                   d2fbjl2 L:110-213 Immunoglobulin light chain kappa constant domain, CL-kappa                             SCOP domains
               CATH domains 2fbjL01 L:1-107 Immunoglobulins                                                                            2fbjL02 L:108-210 Immunoglobulins                                                                      --- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeee.....eeeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeeeee..eeee...eeeeee......eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee..eee...eeeee.........eeeeeeeeeehhhhhh..eeeeeee.......eeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2fbj L   1 EIVLTQSPAITAASLGQKVTITCSASSSVSSLHWYQQKSGTSPKPWIYEISKLASGVPARFSGSGSGTSYSLTINTMEAEDAAIYYCQQWTYPLITFGAGTKLELKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC 213
                                    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)
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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 2FBJ)

(-) Gene Ontology  (1, 2)

Asymmetric/Biological Unit(hide GO term definitions)
Chain H   (HVM40_MOUSE | P01810)
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.

Chain L   (KV6A5_MOUSE | P01679)
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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