PDB entry 6npn

View 6npn on RCSB PDB site
Description: Crystal Structure of the Human vaccinia-related kinase bound to a N,N-dipropynyl-dihydropteridine-3-hydroxyindazole inhibitor
Class: transferase/transferase inhibitor
Keywords: transferase, protein kinase domain, Structural Genomics, Structural Genomics Consortium, SGC, Transferase-Transferase Inhibitor Complex
Deposited on 2019-01-18, released 2019-02-20
The last revision prior to the SCOPe 2.08 freeze date was dated 2020-01-01, with a file datestamp of 2019-12-27.
Experiment type: XRAY
Resolution: 2.2 Å
R-factor: N/A
AEROSPACI score: 0.27 (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 2.08: d6npna_
  • 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 2.08: d6npnb_
  • 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 2.08: d6npnc_
  • 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 2.08: d6npnd_
  • Heterogens: KWJ, SO4, EDO, PEG, HOH

PDB Chain Sequences:

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

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

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

    Sequence, based on observed residues (ATOM records): (download) 
    >6npnB (B:)
avgeiitdmaaaawkvglpciyladmnssdapcvvkvepsdngplftelkfyqraakpeq
iqkwirtrklkylgvpkywgsglhdyrfmimdrfgsdlqkiyeanakrfsrktvlqlslr
ildileyiheheyvhgdikasnlllnyknpdqvylvdyglayrycpegvhkayaadpkrc
hdgtieftsidahngvapsrrgdleilgycmiqwltghlpwednlkdpkyvrdskiryre
niaslmdkcfpaanapgeiakymetvklldytekplyenlrdillqglkaigskddgkld
l

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

    Sequence, based on observed residues (ATOM records): (download) 
    >6npnC (C:)
eqfavgeiitdmaaaawkvglpiciyladmnssesvgsdapcvvkvepsdngplftelkf
yqraakpeqiqkwirtrklkylgvpkywgsglhdkngksyrfmimdrfgsdlqkiyeana
krfsrktvlqlslrildileyiheheyvhgdikasnlllnyknpdqvylvdyglayrycp
egvhkayaadpkrchdgtieftsidahngvapsrrgdleilgycmiqwltghlpwednlk
dpkyvrdskiryreniaslmdkcfpaanapgeiakymetvklldytekplyenlrdillq
glkaigskddgkldl

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

    Sequence, based on observed residues (ATOM records): (download) 
    >6npnD (D:)
qfavgeiitdmaaaawkvglpiciyladmnsvgsdapcvvkvepsdngplftelkfyqra
akpeqiqkwirtrklkylgvpkywgsglhdkngksyrfmimdrfgsdlqkiyeanakrfs
rktvlqlslrildileyiheheyvhgdikasnlllnyknpdqvylvdyglayrycpegvh
kayaadpkrchdgtieftsidahngvapsrrgdleilgycmiqwltghlpwednlkdpky
vrdskiryreniaslmdkcfpaanapgeiakymetvklldytekplyenlrdillqglka
igskddgkldl