PDB entry 6iw2

View 6iw2 on RCSB PDB site
Description: Crystal structure of 5A ScFv in complex with YFV-17D sE in prefusion state
Class: viral protein/immune system
Keywords: Yellow fever virus, Neutralizing monoclonal antibody, Envelope protein, Flavivirus, VIRAL PROTEIN, VIRAL PROTEIN-IMMUNE SYSTEM complex
Deposited on 2018-12-04, released 2019-02-13
The last revision prior to the SCOPe 2.07 freeze date was dated 2019-02-13, with a file datestamp of 2019-02-08.
Experiment type: XRAY
Resolution: 2.9 Å
R-factor: N/A
AEROSPACI score: 0.15 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: Envelope protein E
    Species: Yellow fever virus (strain 17D vaccine) [TaxId:11090]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d6iw2a1, d6iw2a2
  • Chain 'B':
    Compound: Heavy chain of monoclonal antibody 5A
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 6IW2 (0-119)
    Domains in SCOPe 2.07: d6iw2b_
  • Chain 'C':
    Compound: Light chain of monoclonal antibody 5A
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 6IW2 (0-106)
    Domains in SCOPe 2.07: d6iw2c_
  • Chain 'D':
    Compound: Envelope protein E
    Species: Yellow fever virus (strain 17D vaccine) [TaxId:11090]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d6iw2d1, d6iw2d2
  • Chain 'E':
    Compound: Heavy chain of monoclonal antibody 5A
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 6IW2 (0-119)
    Domains in SCOPe 2.07: d6iw2e_
  • Chain 'F':
    Compound: Light chain of monoclonal antibody 5A
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 6IW2 (0-106)
    Domains in SCOPe 2.07: d6iw2f_
  • Chain 'G':
    Compound: Envelope protein E
    Species: Yellow fever virus (strain 17D vaccine) [TaxId:11090]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d6iw2g1, d6iw2g2
  • Chain 'H':
    Compound: Heavy chain of monoclonal antibody 5A
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 6IW2 (0-119)
    Domains in SCOPe 2.07: d6iw2h_
  • Chain 'I':
    Compound: Light chain of monoclonal antibody 5A
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 6IW2 (0-106)
    Domains in SCOPe 2.07: d6iw2i_
  • Chain 'J':
    Compound: Envelope protein E
    Species: Yellow fever virus (strain 17D vaccine) [TaxId:11090]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d6iw2j1, d6iw2j2
  • Chain 'K':
    Compound: Heavy chain of monoclonal antibody 5A
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 6IW2 (0-119)
    Domains in SCOPe 2.07: d6iw2k_
  • Chain 'L':
    Compound: Light chain of monoclonal antibody 5A
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 6IW2 (Start-106)
    Domains in SCOPe 2.07: d6iw2l_
  • Chain 'M':
    Compound: Envelope protein E
    Species: Yellow fever virus (strain 17D vaccine) [TaxId:11090]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d6iw2m1, d6iw2m2
  • Chain 'N':
    Compound: Heavy chain of monoclonal antibody 5A
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 6IW2 (0-119)
    Domains in SCOPe 2.07: d6iw2n_
  • Chain 'O':
    Compound: Light chain of monoclonal antibody 5A
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 6IW2 (0-106)
    Domains in SCOPe 2.07: d6iw2o_
  • Chain 'P':
    Compound: Envelope protein E
    Species: Yellow fever virus (strain 17D vaccine) [TaxId:11090]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d6iw2p1, d6iw2p2
  • Chain 'Q':
    Compound: Heavy chain of monoclonal antibody 5A
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 6IW2 (0-119)
    Domains in SCOPe 2.07: d6iw2q_
  • Chain 'R':
    Compound: Light chain of monoclonal antibody 5A
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 6IW2 (0-106)
    Domains in SCOPe 2.07: d6iw2r_

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download)
    >6iw2A (A:)
    ahcigitdrdfiegvhggtwvsatleqdkcvtvmapdkpsldisletvaidrpaevrkvc
    ynavlthvkindkcpstgeahlaeenegdnackrtysdrgwgngcglfgkgsivacakft
    caksmslfevdqtkiqyviraqlhvgakqenwntdiktlkfdalsgsqevefigygkatl
    ecqvqtavdfgnsyiaemeteswivdrqwaqdltlpwqsgsggvwremhhlvefepphaa
    tirvlalgnqegslktaltgamrvtkdtndnnlyklhgghvscrvklsaltlkgtsykic
    tdkmffvknptdtghgtvvmqvkvskgapcripvivaddltaainkgilvtvnpiastnd
    devlievnppfgdsyiivgrgdsrltyqwhkegss
    

    Sequence, based on observed residues (ATOM records): (download)
    >6iw2A (A:)
    ahcigitdrdfiegvhggtwvsatleqdkcvtvmapdkpsldisletvaidrpaevrkvc
    ynavlthvkindkcpstgeahlaeenegdnackrtysdrgwgngcglfgkgsivacakft
    caksmslfevdqtkiqyviraqlhvgakqenwntdiktlkfdagsqevefigygkatlec
    qvqtavdfgnsyiaemeteswivdrqwaqdltlpwqsgsggvwremhhlvefepphaati
    rvlalgnqegslktaltgamrvtkdtlyklhgghvscrvklsaltlkgtsykictdkmff
    vknptdtghgtvvmqvkvskgapcripvivaddltaainkgilvtvnpiastnddevlie
    vnppfgdsyiivgrgdsrltyqwhke
    

  • Chain 'B':
    Sequence; same for both SEQRES and ATOM records: (download)
    >6iw2B (B:)
    evqlvesgprlvkpsetlsltctvsggstynhhwswirqppgrglewigyisysgksnyn
    pslksrvtislepsttqfslklnsltaadtavyycareyrddtnyyyysldvwgpgtmvt
    

  • Chain 'C':
    Sequence; same for both SEQRES and ATOM records: (download)
    >6iw2C (C:)
    qivmtqspstlsasvgdrvtitcrasqsigswlawyqqkpgkapklliykasslesgvps
    rfsgsgsgteftltisslqpedfatyycqqynnysytfgpgtkleik
    

  • Chain 'D':
    Sequence, based on SEQRES records: (download)
    >6iw2D (D:)
    ahcigitdrdfiegvhggtwvsatleqdkcvtvmapdkpsldisletvaidrpaevrkvc
    ynavlthvkindkcpstgeahlaeenegdnackrtysdrgwgngcglfgkgsivacakft
    caksmslfevdqtkiqyviraqlhvgakqenwntdiktlkfdalsgsqevefigygkatl
    ecqvqtavdfgnsyiaemeteswivdrqwaqdltlpwqsgsggvwremhhlvefepphaa
    tirvlalgnqegslktaltgamrvtkdtndnnlyklhgghvscrvklsaltlkgtsykic
    tdkmffvknptdtghgtvvmqvkvskgapcripvivaddltaainkgilvtvnpiastnd
    devlievnppfgdsyiivgrgdsrltyqwhkegss
    

    Sequence, based on observed residues (ATOM records): (download)
    >6iw2D (D:)
    ahcigitdrdfiegvhggtwvsatleqdkcvtvmapdkpsldisletvaidrpaevrkvc
    ynavlthvkindkcpstgeahlaeenegdnackrtysdrgwgngcglfgkgsivacakft
    caksmslfevdqtkiqyviraqlhvgakqenwntdiktlkfdalsgsqevefigygkatl
    ecqvqtavdfgnsyiaemeteswivdrqwaqdltlpwqsgsggvwremhhlvefepphaa
    tirvlalgnqegslktaltgamrvtkdtlyklhgghvscrvklsaltlkgtsykictdkm
    ffvknptdtghgtvvmqvkvskgapcripvivaddltaainkgilvtvnpiastnddevl
    ievnppfgdsyiivgrgdsrltyqwhke
    

  • Chain 'E':
    Sequence; same for both SEQRES and ATOM records: (download)
    >6iw2E (E:)
    evqlvesgprlvkpsetlsltctvsggstynhhwswirqppgrglewigyisysgksnyn
    pslksrvtislepsttqfslklnsltaadtavyycareyrddtnyyyysldvwgpgtmvt
    

  • Chain 'F':
    Sequence; same for both SEQRES and ATOM records: (download)
    >6iw2F (F:)
    qivmtqspstlsasvgdrvtitcrasqsigswlawyqqkpgkapklliykasslesgvps
    rfsgsgsgteftltisslqpedfatyycqqynnysytfgpgtkleik
    

  • Chain 'G':
    Sequence, based on SEQRES records: (download)
    >6iw2G (G:)
    ahcigitdrdfiegvhggtwvsatleqdkcvtvmapdkpsldisletvaidrpaevrkvc
    ynavlthvkindkcpstgeahlaeenegdnackrtysdrgwgngcglfgkgsivacakft
    caksmslfevdqtkiqyviraqlhvgakqenwntdiktlkfdalsgsqevefigygkatl
    ecqvqtavdfgnsyiaemeteswivdrqwaqdltlpwqsgsggvwremhhlvefepphaa
    tirvlalgnqegslktaltgamrvtkdtndnnlyklhgghvscrvklsaltlkgtsykic
    tdkmffvknptdtghgtvvmqvkvskgapcripvivaddltaainkgilvtvnpiastnd
    devlievnppfgdsyiivgrgdsrltyqwhkegss
    

    Sequence, based on observed residues (ATOM records): (download)
    >6iw2G (G:)
    ahcigitdrdfiegvhggtwvsatleqdkcvtvmapdkpsldisletvaidrpaevrkvc
    ynavlthvkindkcpstgeahlaeenegdnackrtysdrgwgngcglfgkgsivacakft
    caksmslfevdqtkiqyviraqlhvgakqenwntdiktlkfdalsgsqevefigygkatl
    ecqvqtavdfgnsyiaemeteswivdrqwaqdltlpwqsgsggvwremhhlvefepphaa
    tirvlalgnqegslktaltgamrvtkdtlyklhgghvscrvklsaltlkgtsykictdkm
    ffvknptdtghgtvvmqvkvskgapcripvivaddltaainkgilvtvnpiastnddevl
    ievnppfgdsyiivgrgdsrltyqwhke
    

  • Chain 'H':
    Sequence; same for both SEQRES and ATOM records: (download)
    >6iw2H (H:)
    evqlvesgprlvkpsetlsltctvsggstynhhwswirqppgrglewigyisysgksnyn
    pslksrvtislepsttqfslklnsltaadtavyycareyrddtnyyyysldvwgpgtmvt
    

  • Chain 'I':
    Sequence; same for both SEQRES and ATOM records: (download)
    >6iw2I (I:)
    qivmtqspstlsasvgdrvtitcrasqsigswlawyqqkpgkapklliykasslesgvps
    rfsgsgsgteftltisslqpedfatyycqqynnysytfgpgtkleik
    

  • Chain 'J':
    Sequence, based on SEQRES records: (download)
    >6iw2J (J:)
    ahcigitdrdfiegvhggtwvsatleqdkcvtvmapdkpsldisletvaidrpaevrkvc
    ynavlthvkindkcpstgeahlaeenegdnackrtysdrgwgngcglfgkgsivacakft
    caksmslfevdqtkiqyviraqlhvgakqenwntdiktlkfdalsgsqevefigygkatl
    ecqvqtavdfgnsyiaemeteswivdrqwaqdltlpwqsgsggvwremhhlvefepphaa
    tirvlalgnqegslktaltgamrvtkdtndnnlyklhgghvscrvklsaltlkgtsykic
    tdkmffvknptdtghgtvvmqvkvskgapcripvivaddltaainkgilvtvnpiastnd
    devlievnppfgdsyiivgrgdsrltyqwhkegss
    

    Sequence, based on observed residues (ATOM records): (download)
    >6iw2J (J:)
    ahcigitdrdfiegvhggtwvsatleqdkcvtvmapdkpsldisletvaidrpaevrkvc
    ynavlthvkindkcpstgeahlaeenegdnackrtysdrgwgngcglfgkgsivacakft
    caksmslfevdqtkiqyviraqlhvgakqenwntdiktlkfdalsgsqevefigygkatl
    ecqvqtavdfgnsyiaemeteswivdrqwaqdltlpwqsgsggvwremhhlvefepphaa
    tirvlalgnqegslktaltgamrvtkdlyklhgghvscrvklsaltlkgtsykictdkmf
    fvknptdtghgtvvmqvkvskgapcripvivaddltaainkgilvtvnpiastnddevli
    evnppfgdsyiivgrgdsrltyqwhke
    

  • Chain 'K':
    Sequence; same for both SEQRES and ATOM records: (download)
    >6iw2K (K:)
    evqlvesgprlvkpsetlsltctvsggstynhhwswirqppgrglewigyisysgksnyn
    pslksrvtislepsttqfslklnsltaadtavyycareyrddtnyyyysldvwgpgtmvt
    

  • Chain 'L':
    Sequence, based on SEQRES records: (download)
    >6iw2L (L:)
    qivmtqspstlsasvgdrvtitcrasqsigswlawyqqkpgkapklliykasslesgvps
    rfsgsgsgteftltisslqpedfatyycqqynnysytfgpgtkleik
    

    Sequence, based on observed residues (ATOM records): (download)
    >6iw2L (L:)
    ivmtqspstlsasvgdrvtitcrasqsigswlawyqqkpgkapklliykasslesgvpsr
    fsgsgsgteftltisslqpedfatyycqqynnysytfgpgtkleik
    

  • Chain 'M':
    Sequence, based on SEQRES records: (download)
    >6iw2M (M:)
    ahcigitdrdfiegvhggtwvsatleqdkcvtvmapdkpsldisletvaidrpaevrkvc
    ynavlthvkindkcpstgeahlaeenegdnackrtysdrgwgngcglfgkgsivacakft
    caksmslfevdqtkiqyviraqlhvgakqenwntdiktlkfdalsgsqevefigygkatl
    ecqvqtavdfgnsyiaemeteswivdrqwaqdltlpwqsgsggvwremhhlvefepphaa
    tirvlalgnqegslktaltgamrvtkdtndnnlyklhgghvscrvklsaltlkgtsykic
    tdkmffvknptdtghgtvvmqvkvskgapcripvivaddltaainkgilvtvnpiastnd
    devlievnppfgdsyiivgrgdsrltyqwhkegss
    

    Sequence, based on observed residues (ATOM records): (download)
    >6iw2M (M:)
    ahcigitdrdfiegvhggtwvsatleqdkcvtvmapdkpsldisletvaidrpaevrkvc
    ynavlthvkindkcpstgeahlaeenegdnackrtysdrgwgngcglfgkgsivacakft
    caksmslfevdqtkiqyviraqlhvgakqenwntdiktlkfdalsgsqevefigygkatl
    ecqvqtavdfgnsyiaemeteswivdrqwaqdltlpwqsgsggvwremhhlvefepphaa
    tirvlalgnqegslktaltgamrvtkdlyklhgghvscrvklsaltlkgtsykictdkmf
    fvknptdtghgtvvmqvkvskgapcripvivaddltaainkgilvtvnpiastnddevli
    evnppfgdsyiivgrgdsrltyqwhke
    

  • Chain 'N':
    Sequence; same for both SEQRES and ATOM records: (download)
    >6iw2N (N:)
    evqlvesgprlvkpsetlsltctvsggstynhhwswirqppgrglewigyisysgksnyn
    pslksrvtislepsttqfslklnsltaadtavyycareyrddtnyyyysldvwgpgtmvt
    

  • Chain 'O':
    Sequence; same for both SEQRES and ATOM records: (download)
    >6iw2O (O:)
    qivmtqspstlsasvgdrvtitcrasqsigswlawyqqkpgkapklliykasslesgvps
    rfsgsgsgteftltisslqpedfatyycqqynnysytfgpgtkleik
    

  • Chain 'P':
    Sequence, based on SEQRES records: (download)
    >6iw2P (P:)
    ahcigitdrdfiegvhggtwvsatleqdkcvtvmapdkpsldisletvaidrpaevrkvc
    ynavlthvkindkcpstgeahlaeenegdnackrtysdrgwgngcglfgkgsivacakft
    caksmslfevdqtkiqyviraqlhvgakqenwntdiktlkfdalsgsqevefigygkatl
    ecqvqtavdfgnsyiaemeteswivdrqwaqdltlpwqsgsggvwremhhlvefepphaa
    tirvlalgnqegslktaltgamrvtkdtndnnlyklhgghvscrvklsaltlkgtsykic
    tdkmffvknptdtghgtvvmqvkvskgapcripvivaddltaainkgilvtvnpiastnd
    devlievnppfgdsyiivgrgdsrltyqwhkegss
    

    Sequence, based on observed residues (ATOM records): (download)
    >6iw2P (P:)
    ahcigitdrdfiegvhggtwvsatleqdkcvtvmapdkpsldisletvaidrpaevrkvc
    ynavlthvkindkcpstgeahlaeenegdnackrtysdrgwgngcglfgkgsivacakft
    caksmslfevdqtkiqyviraqlhvgakqenwntdiktlkfdalsgsqevefigygkatl
    ecqvqtavdfgnsyiaemeteswivdrqwaqdltlpwqsgsggvwremhhlvefepphaa
    tirvlalgnqegslktaltgamrvtkdlyklhgghvscrvklsaltlkgtsykictdkmf
    fvknptdtghgtvvmqvkvskgapcripvivaddltaainkgilvtvnpiastnddevli
    evnppfgdsyiivgrgdsrltyqwhke
    

  • Chain 'Q':
    Sequence; same for both SEQRES and ATOM records: (download)
    >6iw2Q (Q:)
    evqlvesgprlvkpsetlsltctvsggstynhhwswirqppgrglewigyisysgksnyn
    pslksrvtislepsttqfslklnsltaadtavyycareyrddtnyyyysldvwgpgtmvt
    

  • Chain 'R':
    Sequence; same for both SEQRES and ATOM records: (download)
    >6iw2R (R:)
    qivmtqspstlsasvgdrvtitcrasqsigswlawyqqkpgkapklliykasslesgvps
    rfsgsgsgteftltisslqpedfatyycqqynnysytfgpgtkleik