PDB entry 6fmk

View 6fmk on RCSB PDB site
Description: pVHL:EloB:EloC in complex with N-((S)-1-((2S,4R)-4-hydroxy-2-((4-(4-methylthiazol-5-yl)benzyl)carbamothioyl) pyrrolidin-1-yl)-1-thioxopropan-2-yl)acetamide (ligand 4)
Class: ligase
Keywords: protein complex, ubiquitin ligase, hypoxia inducible factor, LIGASE
Deposited on 2018-01-31, released 2018-04-11
The last revision prior to the SCOPe 2.07 freeze date was dated 2018-04-11, with a file datestamp of 2018-04-06.
Experiment type: XRAY
Resolution: 2.75 Å
R-factor: N/A
AEROSPACI score: 0.18 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: Elongin-B
    Species: Homo sapiens [TaxId:9606]
    Gene: ELOB, TCEB2
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d6fmka_
  • Chain 'B':
    Compound: Elongin-C
    Species: Homo sapiens [TaxId:9606]
    Gene: ELOC, TCEB1
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q15369 (1-96)
      • initiating methionine (0)
    Domains in SCOPe 2.07: d6fmkb1, d6fmkb2
  • Chain 'C':
    Compound: von hippel-lindau disease tumor suppressor
    Species: Homo sapiens [TaxId:9606]
    Gene: VHL
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d6fmkc_
  • Chain 'D':
    Compound: Elongin-B
    Species: Homo sapiens [TaxId:9606]
    Gene: ELOB, TCEB2
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d6fmkd_
  • Chain 'E':
    Compound: Elongin-C
    Species: Homo sapiens [TaxId:9606]
    Gene: ELOC, TCEB1
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q15369 (1-96)
      • initiating methionine (0)
    Domains in SCOPe 2.07: d6fmke1, d6fmke2
  • Chain 'F':
    Compound: von hippel-lindau disease tumor suppressor
    Species: Homo sapiens [TaxId:9606]
    Gene: VHL
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d6fmkf_
  • Chain 'G':
    Compound: Elongin-B
    Species: Homo sapiens [TaxId:9606]
    Gene: ELOB, TCEB2
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d6fmkg_
  • Chain 'H':
    Compound: Elongin-C
    Species: Homo sapiens [TaxId:9606]
    Gene: ELOC, TCEB1
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q15369 (1-96)
      • initiating methionine (0)
    Domains in SCOPe 2.07: d6fmkh1, d6fmkh2
  • Chain 'I':
    Compound: von hippel-lindau disease tumor suppressor
    Species: Homo sapiens [TaxId:9606]
    Gene: VHL
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d6fmki_
  • Chain 'J':
    Compound: Elongin-B
    Species: Homo sapiens [TaxId:9606]
    Gene: ELOB, TCEB2
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d6fmkj_
  • Chain 'K':
    Compound: Elongin-C
    Species: Homo sapiens [TaxId:9606]
    Gene: ELOC, TCEB1
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q15369 (1-96)
      • initiating methionine (0)
    Domains in SCOPe 2.07: d6fmkk1, d6fmkk2
  • Chain 'L':
    Compound: von hippel-lindau disease tumor suppressor
    Species: Homo sapiens [TaxId:9606]
    Gene: VHL
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d6fmkl_
  • Heterogens: DV8, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence; same for both SEQRES and ATOM records: (download)
    >6fmkA (A:)
    mdvflmirrhkttiftdakesstvfelkrivegilkrppdeqrlykddqllddgktlgec
    gftsqtarpqapatvglafraddtfealciepfssppelpdvmk
    

  • Chain 'B':
    Sequence, based on SEQRES records: (download)
    >6fmkB (B:)
    mmyvklissdghefivkrehaltsgtikamlsgpgqfaenetnevnfreipshvlskvcm
    yftykvrytnssteipefpiapeialellmaanfldc
    

    Sequence, based on observed residues (ATOM records): (download)
    >6fmkB (B:)
    mmyvklissdghefivkrehaltsgtikamlsnevnfreipshvlskvcmyftykvrytn
    ssteipefpiapeialellmaanfldc
    

  • Chain 'C':
    Sequence, based on SEQRES records: (download)
    >6fmkC (C:)
    gsmeagrprpvlrsvnsrepsqvifcnrsprvvlpvwlnfdgepqpyptlppgtgrrihs
    yrghlwlfrdagthdgllvnqtelfvpslnvdgqpifanitlpvytlkerclqvvrslvk
    penyrrldivrslyedledhpnvqkdlerltqe
    

    Sequence, based on observed residues (ATOM records): (download)
    >6fmkC (C:)
    vlrsvnsrepsqvifcnrsprvvlpvwlnfdgepqpyptlppgtgrrihsyrghlwlfrd
    agthdgllvnqtelfvpslnvdgqpifanitlpvytlkerclqvvrslvkpenyrrldiv
    rslyedledhpnvqkdlerlt
    

  • Chain 'D':
    Sequence, based on SEQRES records: (download)
    >6fmkD (D:)
    mdvflmirrhkttiftdakesstvfelkrivegilkrppdeqrlykddqllddgktlgec
    gftsqtarpqapatvglafraddtfealciepfssppelpdvmk
    

    Sequence, based on observed residues (ATOM records): (download)
    >6fmkD (D:)
    mdvflmirrhkttiftdakesstvfelkrivegilkrppdeqrlykddqllddgktlgec
    gftsqtarpqapatvglafraddtfealciepfssppelpdvm
    

  • Chain 'E':
    Sequence, based on SEQRES records: (download)
    >6fmkE (E:)
    mmyvklissdghefivkrehaltsgtikamlsgpgqfaenetnevnfreipshvlskvcm
    yftykvrytnssteipefpiapeialellmaanfldc
    

    Sequence, based on observed residues (ATOM records): (download)
    >6fmkE (E:)
    mmyvklissdghefivkrehaltsgtikamlsgnetnevnfreipshvlskvcmyftykv
    rytnssteipefpiapeialellmaanfldc
    

  • Chain 'F':
    Sequence, based on SEQRES records: (download)
    >6fmkF (F:)
    gsmeagrprpvlrsvnsrepsqvifcnrsprvvlpvwlnfdgepqpyptlppgtgrrihs
    yrghlwlfrdagthdgllvnqtelfvpslnvdgqpifanitlpvytlkerclqvvrslvk
    penyrrldivrslyedledhpnvqkdlerltqe
    

    Sequence, based on observed residues (ATOM records): (download)
    >6fmkF (F:)
    vlrsvnsrepsqvifcnrsprvvlpvwlnfdgepqpyptlppgtgrrihsyrghlwlfrd
    agthdgllvnqtelfvpslnvdgqpifanitlpvytlkerclqvvrslvkpenyrrldiv
    rslyedledhpnvqkdlerltqe
    

  • Chain 'G':
    Sequence, based on SEQRES records: (download)
    >6fmkG (G:)
    mdvflmirrhkttiftdakesstvfelkrivegilkrppdeqrlykddqllddgktlgec
    gftsqtarpqapatvglafraddtfealciepfssppelpdvmk
    

    Sequence, based on observed residues (ATOM records): (download)
    >6fmkG (G:)
    mdvflmirrhkttiftdakesstvfelkrivegilkrppdeqrlykddqllddgktlgec
    gftsqtarpqapatvglafraddtfealciepfssppelpdvm
    

  • Chain 'H':
    Sequence, based on SEQRES records: (download)
    >6fmkH (H:)
    mmyvklissdghefivkrehaltsgtikamlsgpgqfaenetnevnfreipshvlskvcm
    yftykvrytnssteipefpiapeialellmaanfldc
    

    Sequence, based on observed residues (ATOM records): (download)
    >6fmkH (H:)
    mmyvklissdghefivkrehaltsgtikamlsgtnevnfreipshvlskvcmyftykvry
    tnssteipefpiapeialellmaanfldc
    

  • Chain 'I':
    Sequence, based on SEQRES records: (download)
    >6fmkI (I:)
    gsmeagrprpvlrsvnsrepsqvifcnrsprvvlpvwlnfdgepqpyptlppgtgrrihs
    yrghlwlfrdagthdgllvnqtelfvpslnvdgqpifanitlpvytlkerclqvvrslvk
    penyrrldivrslyedledhpnvqkdlerltqe
    

    Sequence, based on observed residues (ATOM records): (download)
    >6fmkI (I:)
    vlrsvnsrepsqvifcnrsprvvlpvwlnfdgepqpyptlppgtgrrihsyrghlwlfrd
    agthdgllvnqtelfvpslnvdgqpifanitlpvytlkerclqvvrslvkpenyrrldiv
    rslyedledhpnvqkdlerltqe
    

  • Chain 'J':
    Sequence, based on SEQRES records: (download)
    >6fmkJ (J:)
    mdvflmirrhkttiftdakesstvfelkrivegilkrppdeqrlykddqllddgktlgec
    gftsqtarpqapatvglafraddtfealciepfssppelpdvmk
    

    Sequence, based on observed residues (ATOM records): (download)
    >6fmkJ (J:)
    mdvflmirrhkttiftdakesstvfelkrivegilkrppdeqrlykddqllddgktlgec
    gftsqtarpqapatvglafraddtfealciepfssppelpdvm
    

  • Chain 'K':
    Sequence, based on SEQRES records: (download)
    >6fmkK (K:)
    mmyvklissdghefivkrehaltsgtikamlsgpgqfaenetnevnfreipshvlskvcm
    yftykvrytnssteipefpiapeialellmaanfldc
    

    Sequence, based on observed residues (ATOM records): (download)
    >6fmkK (K:)
    mmyvklissdghefivkrehaltsgtikamlstnevnfreipshvlskvcmyftykvryt
    nssteipefpiapeialellmaanfldc
    

  • Chain 'L':
    Sequence, based on SEQRES records: (download)
    >6fmkL (L:)
    gsmeagrprpvlrsvnsrepsqvifcnrsprvvlpvwlnfdgepqpyptlppgtgrrihs
    yrghlwlfrdagthdgllvnqtelfvpslnvdgqpifanitlpvytlkerclqvvrslvk
    penyrrldivrslyedledhpnvqkdlerltqe
    

    Sequence, based on observed residues (ATOM records): (download)
    >6fmkL (L:)
    vlrsvnsrepsqvifcnrsprvvlpvwlnfdgepqpyptlppgtgrrihsyrghlwlfrd
    agthdgllvnqtelfvpslnvdgqpifanitlpvytlkerclqvvrslvkpenyrrldiv
    rslyedledhpnvqkdlerltqe