PDB entry 5yod

View 5yod on RCSB PDB site
Description: Crystal structure of zika virus NS3 protease in complex with a small molecule inhibitor
Class: viral protein/inhibitor
Keywords: Non-structural protein 3, serine protease, zika viral protease, VIRAL PROTEIN-INHIBITOR complex
Deposited on 2017-10-27, released 2018-03-21
The last revision prior to the SCOPe 2.08 freeze date was dated 2018-04-25, with a file datestamp of 2018-04-20.
Experiment type: XRAY
Resolution: 1.9 Å
R-factor: N/A
AEROSPACI score: 0.32 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: NS2B cofactor
    Species: Zika virus [TaxId:64320]
    Database cross-references and differences (RAF-indexed):
    • PDB 5YOD
    Domains in SCOPe 2.08: d5yoda_
  • Chain 'B':
    Compound: NS3 protease
    Species: Zika virus [TaxId:64320]
    Database cross-references and differences (RAF-indexed):
    • PDB 5YOD
    Domains in SCOPe 2.08: d5yodb_
  • Chain 'C':
    Compound: NS2B cofactor
    Species: Zika virus [TaxId:64320]
    Database cross-references and differences (RAF-indexed):
    • PDB 5YOD
    Domains in SCOPe 2.08: d5yodc_
  • Chain 'D':
    Compound: NS3 protease
    Species: Zika virus [TaxId:64320]
    Database cross-references and differences (RAF-indexed):
    • PDB 5YOD
    Domains in SCOPe 2.08: d5yodd_
  • Chain 'E':
    Compound: NS2B cofactor
    Species: Zika virus [TaxId:64320]
    Database cross-references and differences (RAF-indexed):
    • PDB 5YOD
    Domains in SCOPe 2.08: d5yode_
  • Chain 'F':
    Compound: NS3 protease
    Species: Zika virus [TaxId:64320]
    Database cross-references and differences (RAF-indexed):
    • PDB 5YOD
    Domains in SCOPe 2.08: d5yodf_
  • Chain 'G':
    Compound: NS2B cofactor
    Species: Zika virus [TaxId:64320]
    Database cross-references and differences (RAF-indexed):
    • PDB 5YOD
    Domains in SCOPe 2.08: d5yodg_
  • Chain 'H':
    Compound: NS3 protease
    Species: Zika virus [TaxId:64320]
    Database cross-references and differences (RAF-indexed):
    • PDB 5YOD
    Domains in SCOPe 2.08: d5yodh_
  • Heterogens: BEZ, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download) 
    >5yodA (A:)
mtgksvdmyieragditwekdaevtgnsprldvaldesgdfslveedgppmre

    Sequence, based on observed residues (ATOM records): (download) 
    >5yodA (A:)
dmyieragditwekdaevtgnsprldvaldesgdfslv

  • Chain 'B':
    Sequence, based on SEQRES records: (download) 
    >5yodB (B:)
gsgalwdvpapkevkkgettdgvyrvmtrrllgstqvgvgvmqegvfhtmwhvtkgaalr
sgegrldpywgdvkqdlvsycgpwkldaawdglsevqllavppgerakniqtlpgifktk
dgdigavaldypagtsgspildksgrviglygngvvikngsyvsaitqgkreeetpve

    Sequence, based on observed residues (ATOM records): (download) 
    >5yodB (B:)
ettdgvyrvmtrlgstqvgvgvmqegvfhtmwhvtkgaalrsgegrldpywgdvkqdlvs
ycgpwkldaawdglsevqllavppgerakniqtlpgifktkdgdigavaldypagtsgsp
ildksgrviglygngvvikngsyvsaitqgkr

  • Chain 'C':
    Sequence, based on SEQRES records: (download) 
    >5yodC (C:)
mtgksvdmyieragditwekdaevtgnsprldvaldesgdfslveedgppmre

    Sequence, based on observed residues (ATOM records): (download) 
    >5yodC (C:)
dmyieragditwekdaevtgnsprldvaldesgdfslv

  • Chain 'D':
    Sequence, based on SEQRES records: (download) 
    >5yodD (D:)
gsgalwdvpapkevkkgettdgvyrvmtrrllgstqvgvgvmqegvfhtmwhvtkgaalr
sgegrldpywgdvkqdlvsycgpwkldaawdglsevqllavppgerakniqtlpgifktk
dgdigavaldypagtsgspildksgrviglygngvvikngsyvsaitqgkreeetpve

    Sequence, based on observed residues (ATOM records): (download) 
    >5yodD (D:)
ettdgvyrvmtrlgstqvgvgvmqegvfhtmwhvtkgaalrsgegrldpywgdvkqdlvs
ycgpwkldaawdglsevqllavppgerakniqtlpgifktkdgdigavaldypagtsgsp
ildksgrviglygngvvikngsyvsaitqgkr

  • Chain 'E':
    Sequence, based on SEQRES records: (download) 
    >5yodE (E:)
mtgksvdmyieragditwekdaevtgnsprldvaldesgdfslveedgppmre

    Sequence, based on observed residues (ATOM records): (download) 
    >5yodE (E:)
dmyieragditwekdaevtgnsprldvaldesgdfslv

  • Chain 'F':
    Sequence, based on SEQRES records: (download) 
    >5yodF (F:)
gsgalwdvpapkevkkgettdgvyrvmtrrllgstqvgvgvmqegvfhtmwhvtkgaalr
sgegrldpywgdvkqdlvsycgpwkldaawdglsevqllavppgerakniqtlpgifktk
dgdigavaldypagtsgspildksgrviglygngvvikngsyvsaitqgkreeetpve

    Sequence, based on observed residues (ATOM records): (download) 
    >5yodF (F:)
ettdgvyrvmtrlgstqvgvgvmqegvfhtmwhvtkgaalrsgrldpywgdvkqdlvsyc
gpwkldaawdglsevqllavppgerakniqtlpgifktkdgdigavaldypagtsgspil
dksgrviglygngvvikngsyvsaitqgkr

  • Chain 'G':
    Sequence, based on SEQRES records: (download) 
    >5yodG (G:)
mtgksvdmyieragditwekdaevtgnsprldvaldesgdfslveedgppmre

    Sequence, based on observed residues (ATOM records): (download) 
    >5yodG (G:)
dmyieragditwekdaevtgnsprldvaldesgdfslv

  • Chain 'H':
    Sequence, based on SEQRES records: (download) 
    >5yodH (H:)
gsgalwdvpapkevkkgettdgvyrvmtrrllgstqvgvgvmqegvfhtmwhvtkgaalr
sgegrldpywgdvkqdlvsycgpwkldaawdglsevqllavppgerakniqtlpgifktk
dgdigavaldypagtsgspildksgrviglygngvvikngsyvsaitqgkreeetpve

    Sequence, based on observed residues (ATOM records): (download) 
    >5yodH (H:)
ettdgvyrvmtrtqvgvgvmqegvfhtmwhvtkgaalrsgegrldpywgdvkqdlvsycg
pwkldaawdglsevqllavppgerakniqtlpgifktkdgdigavaldypagtsgspild
ksgrviglygngvvikngsyvsaitqgkr