PDB entry 5m1d

View 5m1d on RCSB PDB site
Description: Crystal structure of N-terminally tagged UbiD from E. coli reconstituted with prFMN cofactor
Class: lyase
Keywords: UbiD, decarboxylase, ubiquinone biosynthesis, prFMN binding, lyase
Deposited on 2016-10-07, released 2017-01-11
The last revision prior to the SCOPe 2.06 freeze date was dated 2017-01-11, with a file datestamp of 2017-01-06.
Experiment type: XRAY
Resolution: 2.7 Å
R-factor: N/A
AEROSPACI score: 0.18 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: 3-octaprenyl-4-hydroxybenzoate carboxy-lyase
    Species: Escherichia coli [TaxId:562]
    Gene: ubiD, c4790
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d5m1da1, d5m1da2
  • Chain 'B':
    Compound: 3-octaprenyl-4-hydroxybenzoate carboxy-lyase
    Species: Escherichia coli [TaxId:562]
    Gene: ubiD, c4790
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d5m1db1, d5m1db2
  • Chain 'C':
    Compound: 3-octaprenyl-4-hydroxybenzoate carboxy-lyase
    Species: Escherichia coli [TaxId:562]
    Gene: ubiD, c4790
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d5m1dc1, d5m1dc2
  • Heterogens: MN, 4LU, NA, SO4, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download)
    >5m1dA (A:)
    mgsshhhhhhssglvprgshmdamkyndlrdfltlleqqgelkritlpvdphleiteiad
    rtlraggpallfenpkgysmpvlcnlfgtpkrvamgmgqedvsalrevgkllaflkepep
    pkgfrdlfdklpqfkqvlnmptkrlrgapcqqkivsgddvdlnripimtcwpedaaplit
    wgltvtrgphkerqnlgiyrqqligknklimrwlshrggaldyqewcaahpgerfpvsva
    lgadpatilgavtpvpdtlseyafagllrgtktevvkcisndlevpasaeivlegyieqg
    etapegpygdhtgyynevdsfpvftvthitqredaiyhstytgrppdepavlgvalnevf
    vpilqkqfpeivdfylppegcsyrlavvtikkqyaghakrvmmgvwsflrqfmytkfviv
    cdddvnardwndviwaittrmdpardtvlventpidyldfaspvsglgskmgldatnkwp
    getqrewgrpikkdpdvvahidaiwdelaifnngksa
    

    Sequence, based on observed residues (ATOM records): (download)
    >5m1dA (A:)
    yndlrdfltlleqqgelkritlpvdphleiteiadrtlraggpallfenpkgysmpvlcn
    lfgtpkrvamgmgqedvsalrevgkllaflkkqvlnmptkrlrgapcqqkivsgddvdln
    ripimtcwpedaaplitwgltvtrgphkerqnlgiyrqqligknklimrwlshrggaldy
    qewcaahpgerfpvsvalgadpatilgavtpvpdtlseyafagllrgtktevvkcisndl
    evpasaeivlegyieqgetapegpygdhtgyynevdsfpvftvthitqredaiyhstytg
    rppdepavlgvalnevfvpilqkqfpeivdfylppegcsyrlavvtikkqyaghakrvmm
    gvwsflrqfmytkfvivcdddvnardwndviwaittrmdpardtvlventpidyldfasp
    vsglgskmgldatnkwpgetqrewgrpikkdpdvvahidaiwdelaifn
    

  • Chain 'B':
    Sequence, based on SEQRES records: (download)
    >5m1dB (B:)
    mgsshhhhhhssglvprgshmdamkyndlrdfltlleqqgelkritlpvdphleiteiad
    rtlraggpallfenpkgysmpvlcnlfgtpkrvamgmgqedvsalrevgkllaflkepep
    pkgfrdlfdklpqfkqvlnmptkrlrgapcqqkivsgddvdlnripimtcwpedaaplit
    wgltvtrgphkerqnlgiyrqqligknklimrwlshrggaldyqewcaahpgerfpvsva
    lgadpatilgavtpvpdtlseyafagllrgtktevvkcisndlevpasaeivlegyieqg
    etapegpygdhtgyynevdsfpvftvthitqredaiyhstytgrppdepavlgvalnevf
    vpilqkqfpeivdfylppegcsyrlavvtikkqyaghakrvmmgvwsflrqfmytkfviv
    cdddvnardwndviwaittrmdpardtvlventpidyldfaspvsglgskmgldatnkwp
    getqrewgrpikkdpdvvahidaiwdelaifnngksa
    

    Sequence, based on observed residues (ATOM records): (download)
    >5m1dB (B:)
    yndlrdfltlleqqgelkritlpvdphleiteiadrtlraggpallfenpkgysmpvlcn
    lfgtpkrvamgmgqedvsalrevgkllaflklnmptkrlrgapcqqkivsgddvdlnrip
    imtcwpedaaplitwgltvtrgphkerqnlgiyrqqligknklimrwlshrggaldyqew
    caahpgerfpvsvalgadpatilgavtpvpdtlseyafagllrgtktevvkcisndlevp
    asaeivlegyieqgetapegpygdhtgyynevdsfpvftvthitqredaiyhstytgrpp
    depavlgvalnevfvpilqkqfpeivdfylppegcsyrlavvtikkqyaghakrvmmgvw
    sflrqfmytkfvivcdddvnardwndviwaittrmdpardtvlventpidyldfaspvsg
    lgskmgldatnkwpgetqrewgrpikkdpdvvahidaiwdelaif
    

  • Chain 'C':
    Sequence, based on SEQRES records: (download)
    >5m1dC (C:)
    mgsshhhhhhssglvprgshmdamkyndlrdfltlleqqgelkritlpvdphleiteiad
    rtlraggpallfenpkgysmpvlcnlfgtpkrvamgmgqedvsalrevgkllaflkepep
    pkgfrdlfdklpqfkqvlnmptkrlrgapcqqkivsgddvdlnripimtcwpedaaplit
    wgltvtrgphkerqnlgiyrqqligknklimrwlshrggaldyqewcaahpgerfpvsva
    lgadpatilgavtpvpdtlseyafagllrgtktevvkcisndlevpasaeivlegyieqg
    etapegpygdhtgyynevdsfpvftvthitqredaiyhstytgrppdepavlgvalnevf
    vpilqkqfpeivdfylppegcsyrlavvtikkqyaghakrvmmgvwsflrqfmytkfviv
    cdddvnardwndviwaittrmdpardtvlventpidyldfaspvsglgskmgldatnkwp
    getqrewgrpikkdpdvvahidaiwdelaifnngksa
    

    Sequence, based on observed residues (ATOM records): (download)
    >5m1dC (C:)
    ndlrdfltlleqqgelkritlpvdphleiteiadrtlraggpallfenpkgysmpvlcnl
    fgtpkrvamgmgqedvsalrevgkllaflkepmptkrlqqkivsgddvdlnripimtcwp
    edaaplitwgltvtrgphkerqnlgiyrqqligknklimrwlshrggaldyqewcaahpg
    erfpvsvalgadpatilgavtpvpdtlseyafagllrgtktevvkcisndlevpasaeiv
    legyieqgetapegpygdhtgyynevdsfpvftvthitqredaiyhstytgrppdepavl
    gvalnevfvpilqkqfpeivdfylppegcsyrlavvtikkqyaghakrvmmgvwsflrqf
    mytkfvivcdddvnardwndviwaittrmdpardtvlventpidyldfaspvsglgskmg
    ldatnkwpgetqrewgrpikkdpdvvahidaiwdelaif