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(-) Description

Title :  HIGH RESOLUTION CRYSTAL STRUCTURE OF THE FV FRAGMENT FROM AN ANTI-DANSYL SWITCH VARIANT ANTIBODY IGG2A(S) CRYSTALLIZED AT PH 5.25
 
Authors :  M. Nakasako, H. Takahashi, I. Shimada, Y. Arata
Date :  14 Jul 98  (Deposition) - 26 Jul 99  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.45
Chains :  Asym./Biol. Unit :  H,L
Keywords :  Fv Fragment, Immunoglobulin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Nakasako, H. Takahashi, N. Shimba, I. Shimada, Y. Arata
The Ph-Dependent Structural Variation Of Complementarity-Determining Region H3 In The Crystal Structures Of The Fv Fragment From An Anti-Dansyl Monoclonal Antibody.
J. Mol. Biol. V. 291 117 1999
PubMed-ID: 10438610  |  Reference-DOI: 10.1006/JMBI.1999.2931
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ANTI-DANSYL IMMUNOGLOBULIN IGG2A(S)
    Cell Line: HYBRIDOMA
    Chains: L
    Fragment: FV FRAGMENT (VH AND VL DOMAINS)
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Synonym: ANTI-DANSYL FV FRAGMENT
 
Molecule 2 - ANTI-DANSYL IMMUNOGLOBULIN IGG2A(S)
    Cell Line: HYBRIDOMA
    Chains: H
    Fragment: FV FRAGMENT (VH AND VL DOMAINS)
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Synonym: ANTI-DANSYL FV FRAGMENT

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : HL

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric/Biological Unit (1, 4)
No.NameCountTypeFull Name
1SO44Ligand/IonSULFATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE H:27 , THR H:28 , TYR H:97 , HOH H:570 , HOH H:618 , HOH H:652 , HOH H:682 , ARG L:24BINDING SITE FOR RESIDUE SO4 H 500
2AC2SOFTWARELYS H:75 , ARG H:77 , TYR H:79 , HOH H:608 , HOH H:614 , SER L:26BINDING SITE FOR RESIDUE SO4 H 501
3AC3SOFTWAREHOH H:694 , HIS L:93 , LYS L:103 , GLU L:105 , HOH L:117 , HOH L:128 , HOH L:139 , HOH L:214 , HOH L:256BINDING SITE FOR RESIDUE SO4 H 502
4AC4SOFTWAREPHE H:27 , PHE H:29 , SER H:30 , ARG H:76 , HOH H:599 , HOH H:609 , HOH H:632 , HOH H:663 , HOH L:283BINDING SITE FOR RESIDUE SO4 H 503

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1H:22 -H:92
2L:23 -L:88

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Thr L:7 -Pro L:8
2Val L:94 -Pro L:95

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1DLF)

(-) 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:120
                                                                                                                                                        
               SCOP domains d1dlfh_ H: Immunoglobulin heavy chain variable domain, VH                                                                SCOP domains
               CATH domains 1dlfH00 H:1-114 Immunoglobulins                                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeee..........eeeeeeee...hhh.eeeeeeee...eeeeeeee..hhh...eee.......eeeeee....eeeeee....hhh.eeeeeeee.............eee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------ Transcript
                 1dlf H   1 EVKLEESGGGLVQPGGSMKLSCATSGFTFSDAWMDWVRQSPEKGLEWVAEIRNKANNHATYYAESVKGRFTISRDDSKRRVYLQMNTLRAEDTGIYYCTGIYYHYPWFAYWGQGTLVTVS 114
                                    10        20        30        40        50  |||   57        67        77     |||84        94       104       114
                                                                              52A||                            82A||                                
                                                                               52B|                             82B|                                
                                                                                52C                              82C                                


Chain L from PDB  Type:PROTEIN  Length:113
 aligned with KV2A7_MOUSE | P01631 from UniProtKB/Swiss-Prot  Length:113

    Alignment length:113
                                    10        20        30        40        50        60        70        80        90       100       110   
          KV2A7_MOUSE     1 DVVMTQTPLSLPVSLGDQASISCRSSQSLVHSNGNTYLNWYLQKAGQSPKLLIYKVSNRFSGVPDRFSGSGSGTDFTLKISRVEAEDLGIYFCSQTTHVPPTFGGGTKLEIKR 113
               SCOP domains d1dlfl_ L: Immunoglobulin light chain kappa variable domain, VL-kappa                                             SCOP domains
               CATH domains 1dlfL00 L:1-108 Immunoglobulins                                                                                   CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee............eeeeee......eeee.............eeeeee..eeeeee....hhh.eeeeeee...........eeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------- Transcript
                 1dlf L   1 DVVMTQTPLSLPVSLGNQASISCRSSQSLVHSNGNTYLHWYLQKPGQSPKLLIYKVSNRFSGVPDRFSGSGSGTDFTLKISRVEAEDLGVYFCSQSTHVPFTFGSGTKLEIKR 108
                                    10        20       27C||      35        45        55        65        75        85        95       105   
                                                     27A||||                                                                                 
                                                      27B|||                                                                                 
                                                       27C||                                                                                 
                                                        27D|                                                                                 
                                                         27E
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (1, 1)

Asymmetric/Biological Unit(hide GO term definitions)
Chain L   (KV2A7_MOUSE | P01631)
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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 Related Entries

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

UniProtKB/Swiss-Prot
        KV2A7_MOUSE | P01631: 1bfv 1cfv 1maj 1mak 1n4x 1svz 1wz1 2bfv 2dlf 2hkf 2hkh 2ipt 2iqa 2o5x 2o5y 2o5z 2r0w 2vq1

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1DLF)