PDB entry 5gn6

View 5gn6 on RCSB PDB site
Description: Crystal structure of glycerol kinase from Trypanosoma brucei gambiense complexed with cumarin derivative-17b
Class: transferase
Keywords: Glycerol kinase, inhibitor, drug, African trypanosomes, TRANSFERASE
Deposited on 2016-07-19, released 2017-07-26
The last revision prior to the SCOPe 2.07 freeze date was dated 2017-09-06, with a file datestamp of 2017-09-01.
Experiment type: XRAY
Resolution: 2.5 Å
R-factor: N/A
AEROSPACI score: 0.2 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: glycerol kinase
    Species: Trypanosoma brucei gambiense [TaxId:31285]
    Gene: gk
    Database cross-references and differences (RAF-indexed):
    • Uniprot D3KVM3 (2-End)
      • expression tag (0-1)
    Domains in SCOPe 2.07: d5gn6a1, d5gn6a2, d5gn6a3
  • Chain 'B':
    Compound: glycerol kinase
    Species: Trypanosoma brucei gambiense [TaxId:31285]
    Gene: gk
    Database cross-references and differences (RAF-indexed):
    • Uniprot D3KVM3 (2-End)
      • expression tag (0-1)
    Domains in SCOPe 2.07: d5gn6b1, d5gn6b2, d5gn6b3
  • Chain 'C':
    Compound: glycerol kinase
    Species: Trypanosoma brucei gambiense [TaxId:31285]
    Gene: gk
    Database cross-references and differences (RAF-indexed):
    • Uniprot D3KVM3 (2-End)
      • expression tag (0-1)
    Domains in SCOPe 2.07: d5gn6c1, d5gn6c2, d5gn6c3
  • Chain 'D':
    Compound: glycerol kinase
    Species: Trypanosoma brucei gambiense [TaxId:31285]
    Gene: gk
    Database cross-references and differences (RAF-indexed):
    • Uniprot D3KVM3 (2-End)
      • expression tag (0-1)
    Domains in SCOPe 2.07: d5gn6d1, d5gn6d2, d5gn6d3
  • Heterogens: 6Y0, GOL, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download)
    >5gn6A (A:)
    atmkyvgsidqgttstrfiifderqrpvsvhqvphtqhtphpgwlehdpmeifrsackcm
    svaiaklrqkdasfrkieaigitnqrettvawdrvtkeplcyapvwndlrtyditkkvta
    elgggdsmfaskitglpvstyfaafkmrwmlenvpavadacrrgtlcfgtidtwlmykls
    ggkafvtdvtnasrtflmdlrtrkwspelceklkipmetlpeirsnselfgyvetdecgv
    aaalnertpimgsigdqqsalfgnmcfekgeakntygtgcfllmnvgeearfskhgllst
    vgfqvgrdgpcyyalegaiacagatvewmrrnmnlfshiteceklarsvpgtqgivfvpa
    fsgllapywdpsargtivgmtlkttrahviraalqaialqlndvvgsmkrdaglnlsslr
    vdgglskngllmeiqasllgvdilvpsmhettalgaalcaglaagvwtsleevkavsrre
    nswktvspsgsamereamiaewrealkrtkwakl
    

    Sequence, based on observed residues (ATOM records): (download)
    >5gn6A (A:)
    atmkyvgsidqgttstrfiifderqrpvsvhqvphtqhtphpgwlehdpmeifrsackcm
    svaiaklrqkdasfrkieaigitnqrettvawdrvtkeplcyapvwndlrtyditkkvta
    elgggdsmfaskitglpvstyfaafkmrwmlenvpavadacrrgtlcfgtidtwlmykls
    ggkafvtdvtnasrtflmdlrtrkwspelceklkipmetlpeirsnselfgyvetdecgv
    aaalnertpimgsigdqqsalfgnmcfekgeakntygtgcfllmnvgeearfskhgllst
    vgfqvgrdgpcyyalegaiacagatvewmrrnmnlfshiteceklarsvpgtqgivfvpa
    fsgllapywdpsargtivgmtlkttrahviraalqaialqlndvvgsmkrdaglnlsslr
    vdgglskngllmeiqasllgvdilvpsmhettalgaalcaglaagvwtsleevkavsrre
    nswktvspsgsamereamiaewrealkrtkwak
    

  • Chain 'B':
    Sequence, based on SEQRES records: (download)
    >5gn6B (B:)
    atmkyvgsidqgttstrfiifderqrpvsvhqvphtqhtphpgwlehdpmeifrsackcm
    svaiaklrqkdasfrkieaigitnqrettvawdrvtkeplcyapvwndlrtyditkkvta
    elgggdsmfaskitglpvstyfaafkmrwmlenvpavadacrrgtlcfgtidtwlmykls
    ggkafvtdvtnasrtflmdlrtrkwspelceklkipmetlpeirsnselfgyvetdecgv
    aaalnertpimgsigdqqsalfgnmcfekgeakntygtgcfllmnvgeearfskhgllst
    vgfqvgrdgpcyyalegaiacagatvewmrrnmnlfshiteceklarsvpgtqgivfvpa
    fsgllapywdpsargtivgmtlkttrahviraalqaialqlndvvgsmkrdaglnlsslr
    vdgglskngllmeiqasllgvdilvpsmhettalgaalcaglaagvwtsleevkavsrre
    nswktvspsgsamereamiaewrealkrtkwakl
    

    Sequence, based on observed residues (ATOM records): (download)
    >5gn6B (B:)
    atmkyvgsidqgttstrfiifderqrpvsvhqvphtqhtphpgwlehdpmeifrsackcm
    svaiaklrqkdasfrkieaigitnqrettvawdrvtkeplcyapvwndlrtyditkkvta
    elgggdsmfaskitglpvstyfaafkmrwmlenvpavadacrrgtlcfgtidtwlmykls
    ggkafvtdvtnasrtflmdlrtrkwspelceklkipmetlpeirsnselfgyvetdecgv
    aaalnertpimgsigdqqsalfgnmcfekgeakntygtgcfllmnvgeearfskhgllst
    vgfqvgrdgpcyyalegaiacagatvewmrrnmnlfshiteceklarsvpgtqgivfvpa
    fsgllapywdpsargtivgmtlkttrahviraalqaialqlndvvgsmkrdaglnlsslr
    vdgglskngllmeiqasllgvdilvpsmhettalgaalcaglaagvwtsleevkavsrre
    nswktvspsgsamereamiaewrealkrtkwak
    

  • Chain 'C':
    Sequence, based on SEQRES records: (download)
    >5gn6C (C:)
    atmkyvgsidqgttstrfiifderqrpvsvhqvphtqhtphpgwlehdpmeifrsackcm
    svaiaklrqkdasfrkieaigitnqrettvawdrvtkeplcyapvwndlrtyditkkvta
    elgggdsmfaskitglpvstyfaafkmrwmlenvpavadacrrgtlcfgtidtwlmykls
    ggkafvtdvtnasrtflmdlrtrkwspelceklkipmetlpeirsnselfgyvetdecgv
    aaalnertpimgsigdqqsalfgnmcfekgeakntygtgcfllmnvgeearfskhgllst
    vgfqvgrdgpcyyalegaiacagatvewmrrnmnlfshiteceklarsvpgtqgivfvpa
    fsgllapywdpsargtivgmtlkttrahviraalqaialqlndvvgsmkrdaglnlsslr
    vdgglskngllmeiqasllgvdilvpsmhettalgaalcaglaagvwtsleevkavsrre
    nswktvspsgsamereamiaewrealkrtkwakl
    

    Sequence, based on observed residues (ATOM records): (download)
    >5gn6C (C:)
    atmkyvgsidqgttstrfiifderqrpvsvhqvphtqhtphpgwlehdpmeifrsackcm
    svaiaklrqkdasfrkieaigitnqrettvawdrvtkeplcyapvwndlrtyditkkvta
    elgggdsmfaskitglpvstyfaafkmrwmlenvpavadacrrgtlcfgtidtwlmykls
    ggkafvtdvtnasrtflmdlrtrkwspelceklkipmetlpeirsnselfgyvetdecgv
    aaalnertpimgsigdqqsalfgnmcfekgeakntygtgcfllmnvgeearfskhgllst
    vgfqvgrdgpcyyalegaiacagatvewmrrnmnlfshiteceklarsvpgtqgivfvpa
    fsgllapywdpsargtivgmtlkttrahviraalqaialqlndvvgsmkrdaglnlsslr
    vdgglskngllmeiqasllgvdilvpsmhettalgaalcaglaagvwtsleevkavsrre
    nswktvspsgsamereamiaewrealkrtkwak
    

  • Chain 'D':
    Sequence, based on SEQRES records: (download)
    >5gn6D (D:)
    atmkyvgsidqgttstrfiifderqrpvsvhqvphtqhtphpgwlehdpmeifrsackcm
    svaiaklrqkdasfrkieaigitnqrettvawdrvtkeplcyapvwndlrtyditkkvta
    elgggdsmfaskitglpvstyfaafkmrwmlenvpavadacrrgtlcfgtidtwlmykls
    ggkafvtdvtnasrtflmdlrtrkwspelceklkipmetlpeirsnselfgyvetdecgv
    aaalnertpimgsigdqqsalfgnmcfekgeakntygtgcfllmnvgeearfskhgllst
    vgfqvgrdgpcyyalegaiacagatvewmrrnmnlfshiteceklarsvpgtqgivfvpa
    fsgllapywdpsargtivgmtlkttrahviraalqaialqlndvvgsmkrdaglnlsslr
    vdgglskngllmeiqasllgvdilvpsmhettalgaalcaglaagvwtsleevkavsrre
    nswktvspsgsamereamiaewrealkrtkwakl
    

    Sequence, based on observed residues (ATOM records): (download)
    >5gn6D (D:)
    atmkyvgsidqgttstrfiifderqrpvsvhqvphtqhtphpgwlehdpmeifrsackcm
    svaiaklrqkdasfrkieaigitnqrettvawdrvtkeplcyapvwndlrtyditkkvta
    elgggdsmfaskitglpvstyfaafkmrwmlenvpavadacrrgtlcfgtidtwlmykls
    ggkafvtdvtnasrtflmdlrtrkwspelceklkipmetlpeirsnselfgyvetdecgv
    aaalnertpimgsigdqqsalfgnmcfekgeakntygtgcfllmnvgeearfskhgllst
    vgfqvgrdgpcyyalegaiacagatvewmrrnmnlfshiteceklarsvpgtqgivfvpa
    fsgllapywdpsargtivgmtlkttrahviraalqaialqlndvvgsmkrdaglnlsslr
    vdgglskngllmeiqasllgvdilvpsmhettalgaalcaglaagvwtsleevkavsrre
    nswktvspsgsamereamiaewrealkrtkwak