PDB entry 4dz6

View 4dz6 on RCSB PDB site
Description: Transition state mimic of nucleoside-diphosphate kinase from borrelia burgdorferi with bound vanadate and adp
Class: transferase
Keywords: SSGCID, NIAID, NUCLEOSIDE DIPHOSPHATE KINASE, KINASE, VANADATE, TRANSITION STATE MIMIC, TRANSITION STATE ANALOG, TRANSFERASE, Structural Genomics, Seattle Structural Genomics Center for Infectious Disease
Deposited on 2012-02-29, released 2012-03-14
The last revision prior to the SCOPe 2.08 freeze date was dated 2018-06-13, with a file datestamp of 2018-06-08.
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: Nucleoside diphosphate kinase
    Species: Borrelia burgdorferi [TaxId:139]
    Gene: ndk, BB_0463
    Database cross-references and differences (RAF-indexed):
    • Uniprot O51419 (23-189)
      • expression tag (22)
    Domains in SCOPe 2.08: d4dz6a1, d4dz6a2
  • Chain 'B':
    Compound: Nucleoside diphosphate kinase
    Species: Borrelia burgdorferi [TaxId:139]
    Gene: ndk, BB_0463
    Database cross-references and differences (RAF-indexed):
    • Uniprot O51419 (23-189)
      • expression tag (22)
    Domains in SCOPe 2.08: d4dz6b1, d4dz6b2
  • Chain 'C':
    Compound: Nucleoside diphosphate kinase
    Species: Borrelia burgdorferi [TaxId:139]
    Gene: ndk, BB_0463
    Database cross-references and differences (RAF-indexed):
    • Uniprot O51419 (23-189)
      • expression tag (22)
    Domains in SCOPe 2.08: d4dz6c1, d4dz6c2
  • Chain 'D':
    Compound: Nucleoside diphosphate kinase
    Species: Borrelia burgdorferi [TaxId:139]
    Gene: ndk, BB_0463
    Database cross-references and differences (RAF-indexed):
    • Uniprot O51419 (23-189)
      • expression tag (22)
    Domains in SCOPe 2.08: d4dz6d1, d4dz6d2
  • Chain 'E':
    Compound: Nucleoside diphosphate kinase
    Species: Borrelia burgdorferi [TaxId:139]
    Gene: ndk, BB_0463
    Database cross-references and differences (RAF-indexed):
    • Uniprot O51419 (23-189)
      • expression tag (22)
    Domains in SCOPe 2.08: d4dz6e1, d4dz6e2
  • Chain 'F':
    Compound: Nucleoside diphosphate kinase
    Species: Borrelia burgdorferi [TaxId:139]
    Gene: ndk, BB_0463
    Database cross-references and differences (RAF-indexed):
    • Uniprot O51419 (23-189)
      • expression tag (22)
    Domains in SCOPe 2.08: d4dz6f1, d4dz6f2
  • Heterogens: ADP, VN4, EDO, VO4, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download) 
    >4dz6A (A:)
mahhhhhhmgtleaqtqgpgsmsmllqktlcivkpdgvrrgligdvvsrfervglkmvaa
kmlivdeslakkhylyddivfrhseavwnslikfisnspvftfvvegvesievvrklcga
tepklaipgtirgdfsyhsfkysnekgfsiynvihasaneadamreipiwfkdneilnyk
rddecehyyc

    Sequence, based on observed residues (ATOM records): (download) 
    >4dz6A (A:)
smllqktlcivkpdgvrrgligdvvsrfervglkmvaakmlivdeslakkhylyddivfr
hseavwnslikfisnspvftfvvegvesievvrklcgatepklaipgtirgdfsyhsfky
snekgfsiynvihasaneadamreipiwfkdneilnykrddecehyyc

  • Chain 'B':
    Sequence, based on SEQRES records: (download) 
    >4dz6B (B:)
mahhhhhhmgtleaqtqgpgsmsmllqktlcivkpdgvrrgligdvvsrfervglkmvaa
kmlivdeslakkhylyddivfrhseavwnslikfisnspvftfvvegvesievvrklcga
tepklaipgtirgdfsyhsfkysnekgfsiynvihasaneadamreipiwfkdneilnyk
rddecehyyc

    Sequence, based on observed residues (ATOM records): (download) 
    >4dz6B (B:)
smllqktlcivkpdgvrrgligdvvsrfervglkmvaakmlivdeslakkhylyddivfr
hseavwnslikfisnspvftfvvegvesievvrklcgatepklaipgtirgdfsyhsfky
snekgfsiynvihasaneadamreipiwfkdneilnykrddecehyyc

  • Chain 'C':
    Sequence, based on SEQRES records: (download) 
    >4dz6C (C:)
mahhhhhhmgtleaqtqgpgsmsmllqktlcivkpdgvrrgligdvvsrfervglkmvaa
kmlivdeslakkhylyddivfrhseavwnslikfisnspvftfvvegvesievvrklcga
tepklaipgtirgdfsyhsfkysnekgfsiynvihasaneadamreipiwfkdneilnyk
rddecehyyc

    Sequence, based on observed residues (ATOM records): (download) 
    >4dz6C (C:)
smllqktlcivkpdgvrrgligdvvsrfervglkmvaakmlivdeslakkhylyddivfr
hseavwnslikfisnspvftfvvegvesievvrklcgatepklaipgtirgdfsyhsfky
snekgfsiynvihasaneadamreipiwfkdneilnykrddecehyyc

  • Chain 'D':
    Sequence, based on SEQRES records: (download) 
    >4dz6D (D:)
mahhhhhhmgtleaqtqgpgsmsmllqktlcivkpdgvrrgligdvvsrfervglkmvaa
kmlivdeslakkhylyddivfrhseavwnslikfisnspvftfvvegvesievvrklcga
tepklaipgtirgdfsyhsfkysnekgfsiynvihasaneadamreipiwfkdneilnyk
rddecehyyc

    Sequence, based on observed residues (ATOM records): (download) 
    >4dz6D (D:)
smllqktlcivkpdgvrrgligdvvsrfervglkmvaakmlivdeslakkhylyddivfr
hseavwnslikfisnspvftfvvegvesievvrklcgatepklaipgtirgdfsyhsfky
snekgfsiynvihasaneadamreipiwfkdneilnykrddecehyyc

  • Chain 'E':
    Sequence, based on SEQRES records: (download) 
    >4dz6E (E:)
mahhhhhhmgtleaqtqgpgsmsmllqktlcivkpdgvrrgligdvvsrfervglkmvaa
kmlivdeslakkhylyddivfrhseavwnslikfisnspvftfvvegvesievvrklcga
tepklaipgtirgdfsyhsfkysnekgfsiynvihasaneadamreipiwfkdneilnyk
rddecehyyc

    Sequence, based on observed residues (ATOM records): (download) 
    >4dz6E (E:)
smllqktlcivkpdgvrrgligdvvsrfervglkmvaakmlivdeslakkhylyddivfr
hseavwnslikfisnspvftfvvegvesievvrklcgatepklaipgtirgdfsyhsfky
snekgfsiynvihasaneadamreipiwfkdneilnykrddecehyyc

  • Chain 'F':
    Sequence, based on SEQRES records: (download) 
    >4dz6F (F:)
mahhhhhhmgtleaqtqgpgsmsmllqktlcivkpdgvrrgligdvvsrfervglkmvaa
kmlivdeslakkhylyddivfrhseavwnslikfisnspvftfvvegvesievvrklcga
tepklaipgtirgdfsyhsfkysnekgfsiynvihasaneadamreipiwfkdneilnyk
rddecehyyc

    Sequence, based on observed residues (ATOM records): (download) 
    >4dz6F (F:)
smllqktlcivkpdgvrrgligdvvsrfervglkmvaakmlivdeslakkhylyddivfr
hseavwnslikfisnspvftfvvegvesievvrklcgatepklaipgtirgdfsyhsfky
snekgfsiynvihasaneadamreipiwfkdneilnykrddecehyyc