PDB entry 3kj4

View 3kj4 on RCSB PDB site
Description: Structure of rat Nogo receptor bound to 1D9 antagonist antibody
Class: immune system
Keywords: Nogo receptor antagonist antibody, LRR, Cell membrane, Disulfide bond, Glycoprotein, GPI-anchor, Leucine-rich repeat, Lipoprotein, Membrane, Receptor, IMMUNE SYSTEM
Deposited on 2009-11-02, released 2010-09-22
The last revision prior to the SCOPe 2.08 freeze date was dated 2020-07-29, with a file datestamp of 2020-07-04.
Experiment type: XRAY
Resolution: 3.1 Å
R-factor: N/A
AEROSPACI score: 0.12 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: Reticulon-4 receptor
    Species: Rattus norvegicus [TaxId:10116]
    Gene: Nogo Receptor, Nogor, Rtn4r
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d3kj4a_
  • Chain 'B':
    Compound: Fab fragment 1D9 light chain
    Species: Mus musculus [TaxId:10090]
    Database cross-references and differences (RAF-indexed):
    • PDB 3KJ4 (0-218)
    Domains in SCOPe 2.08: d3kj4b1, d3kj4b2
  • Chain 'C':
    Compound: Fab fragment 1D9 heavy chain
    Species: Mus musculus [TaxId:10090]
    Database cross-references and differences (RAF-indexed):
    • PDB 3KJ4 (0-219)
    Domains in SCOPe 2.08: d3kj4c_
  • Chain 'D':
    Compound: Reticulon-4 receptor
    Species: Rattus norvegicus [TaxId:10116]
    Gene: Nogo Receptor, Nogor, Rtn4r
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d3kj4d_
  • Chain 'H':
    Compound: Fab fragment 1D9 heavy chain
    Species: Mus musculus [TaxId:10090]
    Database cross-references and differences (RAF-indexed):
    • PDB 3KJ4 (Start-219)
    Domains in SCOPe 2.08: d3kj4h_
  • Chain 'L':
    Compound: Fab fragment 1D9 light chain
    Species: Mus musculus [TaxId:10090]
    Database cross-references and differences (RAF-indexed):
    • PDB 3KJ4 (0-218)
    Domains in SCOPe 2.08: d3kj4l1, d3kj4l2
  • Heterogens: MAN, ZN, NDG, NAG

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download)
    >3kj4A (A:)
    cpgacvcynepkvttscpqqglqavptgipassqriflhgnrisyvpaasfqscrnltil
    wlhsnalagidaaaftgltlleqldlsdnaqlrvvdpttfrglghlhtlhldrcglqelg
    pglfrglaalqylylqdnnlqalpdntfrdlgnlthlflhgnripsvpehafrglhsldr
    lllhqnhvarvhphafrdlgrlmtlylfannlsmlpaevlvplrslqylrlndnpwvcdc
    rarplwawlqkfrgsssevpcnlpqrlagrdlkrlaasdlegcava
    

    Sequence, based on observed residues (ATOM records): (download)
    >3kj4A (A:)
    cpgacvcynepkvttscpqqglqavptgipassqriflhgnrisyvpaasfqscrnltil
    wlhsnalagidaaaftgltlleqldlsdnaqlrvvdpttfrglghlhtlhldrcglqelg
    pglfrglaalqylylqdnnlqalpdntfrdlgnlthlflhgnripsvpehafrglhsldr
    lllhqnhvarvhphafrdlgrlmtlylfannlsmlpaevlvplrslqylrlndnpwvcdc
    rarplwawlqkfrgsssevpcnlpqrlagrdlkrlaasdlegc
    

  • Chain 'B':
    Sequence; same for both SEQRES and ATOM records: (download)
    >3kj4B (B:)
    divmsqspsslavsagekvtmsckssqsllnsrnrknylawyqqkpgqspkpliywastr
    esgvpdrftgsgsgtdftltissvqaedlavyycmqsynlftfgsgtkleikradaaptv
    sifppsseqltsggasvvcflnnfypkdinvkwkidgserqngvlnswtdqdskdstysm
    sstltltkdeyerhnsytceathktstspivksfnrnec
    

  • Chain 'C':
    Sequence, based on SEQRES records: (download)
    >3kj4C (C:)
    qvqlkesgpglvapsqslsiscsvsgfslssygvhwvrqspgqglewlgviwsggnthyn
    salmsrlsiskensknqvflkmnslqtddtaiyycarvgiyyegawfaywgqgtlvtvsa
    akttppsvyplapgsaaqtnsmvtlgclvkgyfpepvtvtwnsgslssgvhtfpavlqsd
    lytlsssvtvpsstwpsetvtcnvahpasstkvdkkivpr
    

    Sequence, based on observed residues (ATOM records): (download)
    >3kj4C (C:)
    qvqlkesgpglvapsqslsiscsvsgfslssygvhwvrqspgqglewlgviwsggnthyn
    salmsrlsiskensknqvflkmnslqtddtaiyycaryegawfaywgqgtlvtvsaaktt
    ppsvyplapgsaaqtnsmvtlgclvkgyfpepvtvtwnsgslssgvhtfpavlqsdlytl
    sssvtvpsstwpsetvtcnvahpasstkvdkkivpr
    

  • Chain 'D':
    Sequence, based on SEQRES records: (download)
    >3kj4D (D:)
    cpgacvcynepkvttscpqqglqavptgipassqriflhgnrisyvpaasfqscrnltil
    wlhsnalagidaaaftgltlleqldlsdnaqlrvvdpttfrglghlhtlhldrcglqelg
    pglfrglaalqylylqdnnlqalpdntfrdlgnlthlflhgnripsvpehafrglhsldr
    lllhqnhvarvhphafrdlgrlmtlylfannlsmlpaevlvplrslqylrlndnpwvcdc
    rarplwawlqkfrgsssevpcnlpqrlagrdlkrlaasdlegcava
    

    Sequence, based on observed residues (ATOM records): (download)
    >3kj4D (D:)
    cpgacvcynepkvttscpqqglqavptgipassqriflhgnrisyvpaasfqscrnltil
    wlhsnalagidaaaftgltlleqldlsdnaqlrvvdpttfrglghlhtlhldrcglqelg
    pglfrglaalqylylqdnnlqalpdntfrdlgnlthlflhgnripsvpehafrglhsldr
    lllhqnhvarvhphafrdlgrlmtlylfannlsmlpaevlvplrslqylrlndnpwvcdc
    rarplwawlqkfrgsssevpcnlpqrlagrdlkrlaasdlegc
    

  • Chain 'H':
    Sequence, based on SEQRES records: (download)
    >3kj4H (H:)
    qvqlkesgpglvapsqslsiscsvsgfslssygvhwvrqspgqglewlgviwsggnthyn
    salmsrlsiskensknqvflkmnslqtddtaiyycarvgiyyegawfaywgqgtlvtvsa
    akttppsvyplapgsaaqtnsmvtlgclvkgyfpepvtvtwnsgslssgvhtfpavlqsd
    lytlsssvtvpsstwpsetvtcnvahpasstkvdkkivpr
    

    Sequence, based on observed residues (ATOM records): (download)
    >3kj4H (H:)
    vqlkesgpglvapsqslsiscsvsgfslssygvhwvrqspgqglewlgviwsggnthyns
    almsrlsiskensknqvflkmnslqtddtaiyycarvgiyyegawfaywgqgtlvtvsaa
    kttppsvyplapgsaaqtnsmvtlgclvkgyfpepvtvtwnsgslssgvhtfpavlqsdl
    ytlsssvtvpsstwpsetvtcnvahpasstkvdkkivpr
    

  • Chain 'L':
    Sequence; same for both SEQRES and ATOM records: (download)
    >3kj4L (L:)
    divmsqspsslavsagekvtmsckssqsllnsrnrknylawyqqkpgqspkpliywastr
    esgvpdrftgsgsgtdftltissvqaedlavyycmqsynlftfgsgtkleikradaaptv
    sifppsseqltsggasvvcflnnfypkdinvkwkidgserqngvlnswtdqdskdstysm
    sstltltkdeyerhnsytceathktstspivksfnrnec