PDB entry 5kov

View 5kov on RCSB PDB site
Description: crystal structure of the human astrovirus 2 capsid protein spike in complex with a single chain variable fragment of an astrovirus neutralizing antibody at 3.24-a resolution
Deposited on 2016-07-01, released 2016-11-09
The last revision was dated 2020-07-29, with a file datestamp of 2020-07-04.
Experiment type: XRAY
Resolution: 3.25 Å
R-factor: N/A
AEROSPACI score: 0.12 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: Capsid polyprotein VP90
    Species: Human astrovirus-2 [TaxId:12701]
    Gene: ORF2
    Database cross-references and differences (RAF-indexed):
  • Chain 'B':
    Compound: Capsid polyprotein VP90
    Species: Human astrovirus-2 [TaxId:12701]
    Gene: ORF2
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q82446 (Start-217)
      • expression tag (218-220)
  • Chain 'C':
    Compound: PL-2 scFv chain
    Species: Mus musculus [TaxId:10090]
    Database cross-references and differences (RAF-indexed):
    • PDB 5KOV
    • PDB 5KOV (139-End)
  • Chain 'E':
    Compound: PL-2 scFv chain
    Species: Mus musculus [TaxId:10090]
    Database cross-references and differences (RAF-indexed):
    • PDB 5KOV
    • PDB 5KOV (139-End)
  • Chain 'G':
    Compound: Capsid polyprotein VP90
    Species: Human astrovirus-2 [TaxId:12701]
    Gene: ORF2
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q82446 (2-217)
      • expression tag (218-220)
  • Chain 'H':
    Compound: Capsid polyprotein VP90
    Species: Human astrovirus-2 [TaxId:12701]
    Gene: ORF2
    Database cross-references and differences (RAF-indexed):
  • Chain 'I':
    Compound: PL-2 scFv chain
    Species: Mus musculus [TaxId:10090]
    Database cross-references and differences (RAF-indexed):
    • PDB 5KOV
    • PDB 5KOV (139-End)
  • Chain 'K':
    Compound: PL-2 scFv chain
    Species: Mus musculus [TaxId:10090]
    Database cross-references and differences (RAF-indexed):
    • PDB 5KOV
    • PDB 5KOV (139-End)
  • Chain 'M':
    Compound: Capsid polyprotein VP90
    Species: Human astrovirus-2 [TaxId:12701]
    Gene: ORF2
    Database cross-references and differences (RAF-indexed):
  • Chain 'N':
    Compound: Capsid polyprotein VP90
    Species: Human astrovirus-2 [TaxId:12701]
    Gene: ORF2
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q82446 (2-217)
      • expression tag (218)
  • Chain 'O':
    Compound: PL-2 scFv chain
    Species: Mus musculus [TaxId:10090]
    Database cross-references and differences (RAF-indexed):
    • PDB 5KOV
    • PDB 5KOV (139-End)
  • Chain 'Q':
    Compound: PL-2 scFv chain
    Species: Mus musculus [TaxId:10090]
    Database cross-references and differences (RAF-indexed):
    • PDB 5KOV
    • PDB 5KOV
  • Chain 'S':
    Compound: Capsid polyprotein VP90
    Species: Human astrovirus-2 [TaxId:12701]
    Gene: ORF2
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q82446 (2-217)
      • expression tag (218-219)
  • Chain 'T':
    Compound: Capsid polyprotein VP90
    Species: Human astrovirus-2 [TaxId:12701]
    Gene: ORF2
    Database cross-references and differences (RAF-indexed):
  • Chain 'U':
    Compound: PL-2 scFv chain
    Species: Mus musculus [TaxId:10090]
    Database cross-references and differences (RAF-indexed):
    • PDB 5KOV
    • PDB 5KOV (139-End)
  • Chain 'W':
    Compound: PL-2 scFv chain
    Species: Mus musculus [TaxId:10090]
    Database cross-references and differences (RAF-indexed):
    • PDB 5KOV
    • PDB 5KOV
  • Heterogens: NAG

PDB Chain Sequences:
This PDB entry is not classified in SCOPe 2.07, so the chain sequences below are not included in the ASTRAL sequence sets.

  • Chain 'A':
    Sequence, based on SEQRES records:
    >5kovA (A:)
    mggelrvlltvgsimspnsadrqvwlnktltapgtnsndnlvkiahdlghylimqgfmhi
    ktvewytpdfqpsrdptpiagmsvmvnitkkadvyfmkqfknsytnnrhqitsiflikpl
    adfkvqcymsyfkreshdndgvanltvrsmtspetirfqvgewylltsttlkennlpegw
    vwdrvelksdtpyyadqaltyfitpppvdsqilfegntaaaelalvpr
    

    Sequence, based on observed residues (ATOM records):
    >5kovA (A:)
    gelrvlltvgsimspnsadrqvwlnktltapgtnsndnlvkiahdlghylimqgfmhikt
    vewytpdfqpsrdptpiagmsvmvnitkkadvyfmkqfknsytnnrhqitsiflikplad
    fkvqcymsyfkreshdndgvanltvrsmtspetirfqvgewylltsttlkennlpegwvw
    drvelksdtpyyadqaltyfitpppvdsqilfegnt
    

  • Chain 'B':
    Sequence, based on SEQRES records:
    >5kovB (B:)
    mggelrvlltvgsimspnsadrqvwlnktltapgtnsndnlvkiahdlghylimqgfmhi
    ktvewytpdfqpsrdptpiagmsvmvnitkkadvyfmkqfknsytnnrhqitsiflikpl
    adfkvqcymsyfkreshdndgvanltvrsmtspetirfqvgewylltsttlkennlpegw
    vwdrvelksdtpyyadqaltyfitpppvdsqilfegntaaaelalvpr
    

    Sequence, based on observed residues (ATOM records):
    >5kovB (B:)
    elrvlltvgsimspnsadrqvwlnktltapgtnsndnlvkiahdlghylimqgfmhiktv
    ewytpdfqpsrdptpiagmsvmvnitkkadvyfmkqfknsytnnrhqitsiflikpladf
    kvqcymsyfkreshdndgvanltvrsmtspetirfqvgewylltsttlkennlpegwvwd
    rvelksdtpyyadqaltyfitpppvdsqilfegntaaa
    

  • Chain 'C':
    Sequence, based on SEQRES records:
    >5kovC (C:)
    rsdvqlkqsgpglvqpsqslsitctvsgfslidygvhwvrqspgkglewlgviwtggstd
    ynaafisrltiskdnsksqvffkmnslqandtgiyycgrpyygnvmdywgqgtsvtvssg
    tggsggggsggggsgggasdiqmtqttsslsaslgdrvtiscrasqdisnylnwyqqkpd
    gtvklliyytsrlhsgvpsrfsgsgsgtdysltisnleqediatyfcqqgntfpptfggg
    tkleikrlvpr
    

    Sequence, based on observed residues (ATOM records):
    >5kovC (C:)
    dvqlkqsgpglvqpsqslsitctvsgfslidygvhwvrqspgkglewlgviwtggstdyn
    aafisrltiskdnsksqvffkmnslqandtgiyycgrpyygnvmdywgqgtsvtvdiqmt
    qttsslsaslgdrvtiscrasqdisnylnwyqqkpdgtvklliyytsrlhsgvpsrfsgs
    gsgtdysltisnleqediatyfcqqgntfpptfgggtkleikr
    

  • Chain 'E':
    Sequence, based on SEQRES records:
    >5kovE (E:)
    rsdvqlkqsgpglvqpsqslsitctvsgfslidygvhwvrqspgkglewlgviwtggstd
    ynaafisrltiskdnsksqvffkmnslqandtgiyycgrpyygnvmdywgqgtsvtvssg
    tggsggggsggggsgggasdiqmtqttsslsaslgdrvtiscrasqdisnylnwyqqkpd
    gtvklliyytsrlhsgvpsrfsgsgsgtdysltisnleqediatyfcqqgntfpptfggg
    tkleikrlvpr
    

    Sequence, based on observed residues (ATOM records):
    >5kovE (E:)
    dvqlkqsgpglvqpsqslsitctvsgfslidygvhwvrqspgkglewlgviwtggstdyn
    aafisrltiskdnsksqvffkmnslqandtgiyycgrpyygnvmdywgqgtsvtvssdiq
    mtqttsslsaslgdrvtiscrasqdisnylnwyqqkpdgtvklliyytsrlhsgvpsrfs
    gsgsgtdysltisnleqediatyfcqqgntfpptfgggtkleik
    

  • Chain 'G':
    Sequence, based on SEQRES records:
    >5kovG (G:)
    mggelrvlltvgsimspnsadrqvwlnktltapgtnsndnlvkiahdlghylimqgfmhi
    ktvewytpdfqpsrdptpiagmsvmvnitkkadvyfmkqfknsytnnrhqitsiflikpl
    adfkvqcymsyfkreshdndgvanltvrsmtspetirfqvgewylltsttlkennlpegw
    vwdrvelksdtpyyadqaltyfitpppvdsqilfegntaaaelalvpr
    

    Sequence, based on observed residues (ATOM records):
    >5kovG (G:)
    gelrvlltvgsimspnsadrqvwlnktltapgtnsndnlvkiahdlghylimqgfmhikt
    vewytpdfqpsrdptpiagmsvmvnitkkadvyfmkqfknsytnnrhqitsiflikplad
    fkvqcymsyfkreshdndgvanltvrsmtspetirfqvgewylltsttlkennlpegwvw
    drvelksdtpyyadqaltyfitpppvdsqilfegntaaa
    

  • Chain 'H':
    Sequence, based on SEQRES records:
    >5kovH (H:)
    mggelrvlltvgsimspnsadrqvwlnktltapgtnsndnlvkiahdlghylimqgfmhi
    ktvewytpdfqpsrdptpiagmsvmvnitkkadvyfmkqfknsytnnrhqitsiflikpl
    adfkvqcymsyfkreshdndgvanltvrsmtspetirfqvgewylltsttlkennlpegw
    vwdrvelksdtpyyadqaltyfitpppvdsqilfegntaaaelalvpr
    

    Sequence, based on observed residues (ATOM records):
    >5kovH (H:)
    gelrvlltvgsimspnsadrqvwlnktltapgtnsndnlvkiahdlghylimqgfmhikt
    vewytpdfqpsrdptpiagmsvmvnitkkadvyfmkqfknsytnnrhqitsiflikplad
    fkvqcymsyfkreshdndgvanltvrsmtspetirfqvgewylltsttlkennlpegwvw
    drvelksdtpyyadqaltyfitpppvdsqilfegnt
    

  • Chain 'I':
    Sequence, based on SEQRES records:
    >5kovI (I:)
    rsdvqlkqsgpglvqpsqslsitctvsgfslidygvhwvrqspgkglewlgviwtggstd
    ynaafisrltiskdnsksqvffkmnslqandtgiyycgrpyygnvmdywgqgtsvtvssg
    tggsggggsggggsgggasdiqmtqttsslsaslgdrvtiscrasqdisnylnwyqqkpd
    gtvklliyytsrlhsgvpsrfsgsgsgtdysltisnleqediatyfcqqgntfpptfggg
    tkleikrlvpr
    

    Sequence, based on observed residues (ATOM records):
    >5kovI (I:)
    dvqlkqsgpglvqpsqslsitctvsgfslidygvhwvrqspgkglewlgviwtggstdyn
    aafisrltiskdnsksqvffkmnslqandtgiyycgrpyygnvmdywgqgtsvtvssdiq
    mtqttsslsaslgdrvtiscrasqdisnylnwyqqkpdgtvklliyytsrlhsgvpsrfs
    gsgsgtdysltisnleqediatyfcqqgntfpptfgggtkleikr
    

  • Chain 'K':
    Sequence, based on SEQRES records:
    >5kovK (K:)
    rsdvqlkqsgpglvqpsqslsitctvsgfslidygvhwvrqspgkglewlgviwtggstd
    ynaafisrltiskdnsksqvffkmnslqandtgiyycgrpyygnvmdywgqgtsvtvssg
    tggsggggsggggsgggasdiqmtqttsslsaslgdrvtiscrasqdisnylnwyqqkpd
    gtvklliyytsrlhsgvpsrfsgsgsgtdysltisnleqediatyfcqqgntfpptfggg
    tkleikrlvpr
    

    Sequence, based on observed residues (ATOM records):
    >5kovK (K:)
    dvqlkqsgpglvqpsqslsitctvsgfslidygvhwvrqspgkglewlgviwtggstdyn
    aafisrltiskdnsksqvffkmnslqandtgiyycgrpyygnvmdywgqgtsvtvdiqmt
    qttsslsaslgdrvtiscrasqdisnylnwyqqkpdgtvklliyytsrlhsgvpsrfsgs
    gsgtdysltisnleqediatyfcqqgntfpptfgggtkleikr
    

  • Chain 'M':
    Sequence, based on SEQRES records:
    >5kovM (M:)
    mggelrvlltvgsimspnsadrqvwlnktltapgtnsndnlvkiahdlghylimqgfmhi
    ktvewytpdfqpsrdptpiagmsvmvnitkkadvyfmkqfknsytnnrhqitsiflikpl
    adfkvqcymsyfkreshdndgvanltvrsmtspetirfqvgewylltsttlkennlpegw
    vwdrvelksdtpyyadqaltyfitpppvdsqilfegntaaaelalvpr
    

    Sequence, based on observed residues (ATOM records):
    >5kovM (M:)
    gelrvlltvgsimspnsadrqvwlnktltapgtnsndnlvkiahdlghylimqgfmhikt
    vewytpdfqpsrdptpiagmsvmvnitkkadvyfmkqfknsytnnrhqitsiflikplad
    fkvqcymsyfkreshdndgvanltvrsmtspetirfqvgewylltsttlkennlpegwvw
    drvelksdtpyyadqaltyfitpppvdsqilfegnt
    

  • Chain 'N':
    Sequence, based on SEQRES records:
    >5kovN (N:)
    mggelrvlltvgsimspnsadrqvwlnktltapgtnsndnlvkiahdlghylimqgfmhi
    ktvewytpdfqpsrdptpiagmsvmvnitkkadvyfmkqfknsytnnrhqitsiflikpl
    adfkvqcymsyfkreshdndgvanltvrsmtspetirfqvgewylltsttlkennlpegw
    vwdrvelksdtpyyadqaltyfitpppvdsqilfegntaaaelalvpr
    

    Sequence, based on observed residues (ATOM records):
    >5kovN (N:)
    gelrvlltvgsimspnsadrqvwlnktltapgtnsndnlvkiahdlghylimqgfmhikt
    vewytpdfqpsrdptpiagmsvmvnitkkadvyfmkqfknsytnnrhqitsiflikplad
    fkvqcymsyfkreshdndgvanltvrsmtspetirfqvgewylltsttlkennlpegwvw
    drvelksdtpyyadqaltyfitpppvdsqilfegnta
    

  • Chain 'O':
    Sequence, based on SEQRES records:
    >5kovO (O:)
    rsdvqlkqsgpglvqpsqslsitctvsgfslidygvhwvrqspgkglewlgviwtggstd
    ynaafisrltiskdnsksqvffkmnslqandtgiyycgrpyygnvmdywgqgtsvtvssg
    tggsggggsggggsgggasdiqmtqttsslsaslgdrvtiscrasqdisnylnwyqqkpd
    gtvklliyytsrlhsgvpsrfsgsgsgtdysltisnleqediatyfcqqgntfpptfggg
    tkleikrlvpr
    

    Sequence, based on observed residues (ATOM records):
    >5kovO (O:)
    dvqlkqsglvqpsqslsitctvsgfslidygvhwvrqspglewlgviwtggstdynaafi
    srltiskdnsksqvffkmngiyycgrpyygnvmdywgqgtsvtvdiqmtqttsslsaslg
    drvtiscrasqdisnylnwyqqkpdgtvklliyytsrlhsgvpsrfsgsgsgtdysltis
    nleqediatyfcqqgntfpptfgggtkleikr
    

  • Chain 'Q':
    Sequence, based on SEQRES records:
    >5kovQ (Q:)
    rsdvqlkqsgpglvqpsqslsitctvsgfslidygvhwvrqspgkglewlgviwtggstd
    ynaafisrltiskdnsksqvffkmnslqandtgiyycgrpyygnvmdywgqgtsvtvssg
    tggsggggsggggsgggasdiqmtqttsslsaslgdrvtiscrasqdisnylnwyqqkpd
    gtvklliyytsrlhsgvpsrfsgsgsgtdysltisnleqediatyfcqqgntfpptfggg
    tkleikrlvpr
    

    Sequence, based on observed residues (ATOM records):
    >5kovQ (Q:)
    sitctvsgfslidygvhwviwtggstynaafisrltiskdnsksqvffkyycgrpyygnv
    mdywgscrasqdisnylnlliyytsrlhsgvps
    

  • Chain 'S':
    Sequence, based on SEQRES records:
    >5kovS (S:)
    mggelrvlltvgsimspnsadrqvwlnktltapgtnsndnlvkiahdlghylimqgfmhi
    ktvewytpdfqpsrdptpiagmsvmvnitkkadvyfmkqfknsytnnrhqitsiflikpl
    adfkvqcymsyfkreshdndgvanltvrsmtspetirfqvgewylltsttlkennlpegw
    vwdrvelksdtpyyadqaltyfitpppvdsqilfegntaaaelalvpr
    

    Sequence, based on observed residues (ATOM records):
    >5kovS (S:)
    gelrvlltvgsimspnsadrqvwlnktltapgtnsndnlvkiahdlghylimqgfmhikt
    vewytpdfqpsrdptpiagmsvmvnitkkadvyfmkqfknsytnnrhqitsiflikplad
    fkvqcymsyfkreshdndgvanltvrsmtspetirfqvgewylltsttlkennlpegwvw
    drvelksdtpyyadqaltyfitpppvdsqilfegntaa
    

  • Chain 'T':
    Sequence, based on SEQRES records:
    >5kovT (T:)
    mggelrvlltvgsimspnsadrqvwlnktltapgtnsndnlvkiahdlghylimqgfmhi
    ktvewytpdfqpsrdptpiagmsvmvnitkkadvyfmkqfknsytnnrhqitsiflikpl
    adfkvqcymsyfkreshdndgvanltvrsmtspetirfqvgewylltsttlkennlpegw
    vwdrvelksdtpyyadqaltyfitpppvdsqilfegntaaaelalvpr
    

    Sequence, based on observed residues (ATOM records):
    >5kovT (T:)
    gelrvlltvgsimspnsadrqvwlnktltapgtnsndnlvkiahdlghylimqgfmhikt
    vewytpdfqpsrdptpiagmsvmvnitkkadvyfmkqfknsytnnrhqitsiflikplad
    fkvqcymsyfkreshdndgvanltvrsmtspetirfqvgewylltsttlkennlpegwvw
    drvelksdtpyyadqaltyfitpppvdsqilfegnt
    

  • Chain 'U':
    Sequence, based on SEQRES records:
    >5kovU (U:)
    rsdvqlkqsgpglvqpsqslsitctvsgfslidygvhwvrqspgkglewlgviwtggstd
    ynaafisrltiskdnsksqvffkmnslqandtgiyycgrpyygnvmdywgqgtsvtvssg
    tggsggggsggggsgggasdiqmtqttsslsaslgdrvtiscrasqdisnylnwyqqkpd
    gtvklliyytsrlhsgvpsrfsgsgsgtdysltisnleqediatyfcqqgntfpptfggg
    tkleikrlvpr
    

    Sequence, based on observed residues (ATOM records):
    >5kovU (U:)
    dvqlkqsgpglvqpsqslsitctvsgfslidygvhwvrqspgkglewlgviwtggstdyn
    aafisrltiskdnsksqvffkmnslqandtgiyycgrpyygnvmdywgqgtsvtdiqmtq
    ttsslsaslgdrvtiscrasqdisnylnwyqqkpdgtvklliyytsrlhsgvpsrfsgsg
    sgtdysltisnleqediatyfcqqgntfpptfgggtkleikr
    

  • Chain 'W':
    Sequence, based on SEQRES records:
    >5kovW (W:)
    rsdvqlkqsgpglvqpsqslsitctvsgfslidygvhwvrqspgkglewlgviwtggstd
    ynaafisrltiskdnsksqvffkmnslqandtgiyycgrpyygnvmdywgqgtsvtvssg
    tggsggggsggggsgggasdiqmtqttsslsaslgdrvtiscrasqdisnylnwyqqkpd
    gtvklliyytsrlhsgvpsrfsgsgsgtdysltisnleqediatyfcqqgntfpptfggg
    tkleikrlvpr
    

    Sequence, based on observed residues (ATOM records):
    >5kovW (W:)
    kqssitctvsgfslidygvhwewlgviwtggstdynaafisrltiskdnsksqvffkyyc
    grpyygnvmdywgqcrasqdisnylnliyytsrlhcqqgntfppt