PDB entry 6dd4

View 6dd4 on RCSB PDB site
Description: Crystal Structure of the Human vaccinia-related kinase bound to a N,N-dipropyl-dihydropteridine inhibitor
Class: transferase/transferase inhibitor
Keywords: transferase, protein kinase domain, Structural Genomics, Structural Genomics Consortium, SGC, Transferase-Transferase Inhibitor Complex
Deposited on 2018-05-09, released 2018-05-23
The last revision prior to the SCOPe 2.07 freeze date was dated 2018-05-23, with a file datestamp of 2018-05-18.
Experiment type: XRAY
Resolution: 2.1 Å
R-factor: N/A
AEROSPACI score: 0.29 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: Serine/threonine-protein kinase VRK1
    Species: Homo sapiens [TaxId:9606]
    Gene: VRK1
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q99986
      • engineered mutation (33-35)
      • engineered mutation (211)
      • engineered mutation (213-214)
      • engineered mutation (291-292)
      • engineered mutation (294)
    Domains in SCOPe 2.07: d6dd4a_
  • Chain 'B':
    Compound: Serine/threonine-protein kinase VRK1
    Species: Homo sapiens [TaxId:9606]
    Gene: VRK1
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q99986
      • engineered mutation (33-35)
      • engineered mutation (211)
      • engineered mutation (213-214)
      • engineered mutation (291-292)
      • engineered mutation (294)
    Domains in SCOPe 2.07: d6dd4b_
  • Chain 'C':
    Compound: Serine/threonine-protein kinase VRK1
    Species: Homo sapiens [TaxId:9606]
    Gene: VRK1
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q99986
      • engineered mutation (33-35)
      • engineered mutation (211)
      • engineered mutation (213-214)
      • engineered mutation (291-292)
      • engineered mutation (294)
    Domains in SCOPe 2.07: d6dd4c_
  • Chain 'D':
    Compound: Serine/threonine-protein kinase VRK1
    Species: Homo sapiens [TaxId:9606]
    Gene: VRK1
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q99986
      • engineered mutation (33-35)
      • engineered mutation (211)
      • engineered mutation (213-214)
      • engineered mutation (291-292)
      • engineered mutation (294)
    Domains in SCOPe 2.07: d6dd4d_
  • Heterogens: CL, ACT, G6J, SO4, GOL, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download)
    >6dd4A (A:)
    smrvkaaqagrqssakrhlaeqfavgeiitdmaaaawkvglpigqggfgciyladmnsse
    svgsdapcvvkvepsdngplftelkfyqraakpeqiqkwirtrklkylgvpkywgsglhd
    kngksyrfmimdrfgsdlqkiyeanakrfsrktvlqlslrildileyiheheyvhgdika
    snlllnyknpdqvylvdyglayrycpegvhkayaadpkrchdgtieftsidahngvapsr
    rgdleilgycmiqwltghlpwednlkdpkyvrdskiryreniaslmdkcfpaanapgeia
    kymetvklldytekplyenlrdillqglkaigskddgkldlsvvengglkaktitkkraa
    eiee
    

    Sequence, based on observed residues (ATOM records): (download)
    >6dd4A (A:)
    aeqfavgeiitdmaaaawkvglpigciyladmnssesvgsdapcvvkvepsdngplftel
    kfyqraakpeqiqkwirtrklkylgvpkywgsglhdkngksyrfmimdrfgsdlqkiyea
    nakrfsrktvlqlslrildileyiheheyvhgdikasnlllnyknpdqvylvdyglayry
    cpegvhkayaadpkrchdgtieftsidahngvapsrrgdleilgycmiqwltghlpwedn
    lkdpkyvrdskiryreniaslmdkcfpaanapgeiakymetvklldytekplyenlrdil
    lqglkaigskddgkldl
    

  • Chain 'B':
    Sequence, based on SEQRES records: (download)
    >6dd4B (B:)
    smrvkaaqagrqssakrhlaeqfavgeiitdmaaaawkvglpigqggfgciyladmnsse
    svgsdapcvvkvepsdngplftelkfyqraakpeqiqkwirtrklkylgvpkywgsglhd
    kngksyrfmimdrfgsdlqkiyeanakrfsrktvlqlslrildileyiheheyvhgdika
    snlllnyknpdqvylvdyglayrycpegvhkayaadpkrchdgtieftsidahngvapsr
    rgdleilgycmiqwltghlpwednlkdpkyvrdskiryreniaslmdkcfpaanapgeia
    kymetvklldytekplyenlrdillqglkaigskddgkldlsvvengglkaktitkkraa
    eiee
    

    Sequence, based on observed residues (ATOM records): (download)
    >6dd4B (B:)
    favgeiitdmaaaawkvglpigqgciyladmnssgsdapcvvkvepsdngplftelkfyq
    raakpeqiqkwirtrklkylgvpkywgsglhdkyrfmimdrfgsdlqkiyeanakrfsrk
    tvlqlslrildileyiheheyvhgdikasnlllnyknpdqvylvdyglayrycpegvhka
    yaadpkrchdgtieftsidahngvapsrrgdleilgycmiqwltghlpwednlkdpkyvr
    dskiryreniaslmdkcfpaanapgeiakymetvklldytekplyenlrdillqglkaig
    skddgkldl
    

  • Chain 'C':
    Sequence, based on SEQRES records: (download)
    >6dd4C (C:)
    smrvkaaqagrqssakrhlaeqfavgeiitdmaaaawkvglpigqggfgciyladmnsse
    svgsdapcvvkvepsdngplftelkfyqraakpeqiqkwirtrklkylgvpkywgsglhd
    kngksyrfmimdrfgsdlqkiyeanakrfsrktvlqlslrildileyiheheyvhgdika
    snlllnyknpdqvylvdyglayrycpegvhkayaadpkrchdgtieftsidahngvapsr
    rgdleilgycmiqwltghlpwednlkdpkyvrdskiryreniaslmdkcfpaanapgeia
    kymetvklldytekplyenlrdillqglkaigskddgkldlsvvengglkaktitkkraa
    eiee
    

    Sequence, based on observed residues (ATOM records): (download)
    >6dd4C (C:)
    eqfavgeiitdmaaaawkvglpiggciyladmnssesvgsdapcvvkvepsdngplftel
    kfyqraakpeqiqkwirtrklkylgvpkywgsglhdkngksyrfmimdrfgsdlqkiyea
    nakrfsrktvlqlslrildileyiheheyvhgdikasnlllnyknpdqvylvdyglayry
    cpegvhkayaadpkrchdgtieftsidahngvapsrrgdleilgycmiqwltghlpwedn
    lkdpkyvrdskiryreniaslmdkcfpaanapgeiakymetvklldytekplyenlrdil
    lqglkaigskddgkldl
    

  • Chain 'D':
    Sequence, based on SEQRES records: (download)
    >6dd4D (D:)
    smrvkaaqagrqssakrhlaeqfavgeiitdmaaaawkvglpigqggfgciyladmnsse
    svgsdapcvvkvepsdngplftelkfyqraakpeqiqkwirtrklkylgvpkywgsglhd
    kngksyrfmimdrfgsdlqkiyeanakrfsrktvlqlslrildileyiheheyvhgdika
    snlllnyknpdqvylvdyglayrycpegvhkayaadpkrchdgtieftsidahngvapsr
    rgdleilgycmiqwltghlpwednlkdpkyvrdskiryreniaslmdkcfpaanapgeia
    kymetvklldytekplyenlrdillqglkaigskddgkldlsvvengglkaktitkkraa
    eiee
    

    Sequence, based on observed residues (ATOM records): (download)
    >6dd4D (D:)
    qfavgeiitdmaaaawkvglpiggciyladmnsvsdapcvvkvepsdngplftelkfyqr
    aakpeqiqkwirtrklkylgvpkywgsglhdkngksyrfmimdrfgsdlqkiyeanakrf
    srktvlqlslrildileyiheheyvhgdikasnlllnyknpdqvylvdyglayrycpegv
    hkayaadpkrchdgtieftsidahngvapsrrgdleilgycmiqwltghlpwednlkdpk
    yvrdskiryreniaslmdkcfaanapgeiakymetvklldytekplyenlrdillqglka
    igskddgkldl