PDB entry 2idb

View 2idb on RCSB PDB site
Description: Crystal Structure of 3-octaprenyl-4-hydroxybenzoate decarboxylase (UbiD) from Escherichia coli, Northeast Structural Genomics Target ER459.
Class: lyase
Keywords: alpha-beta protein, Structural Genomics, PSI-2, Protein Structure Initiative, Northeast Structural Genomics Consortium, NESG, LYASE
Deposited on 2006-09-14, released 2006-10-24
The last revision prior to the SCOPe 2.08 freeze date was dated 2017-10-18, with a file datestamp of 2017-10-13.
Experiment type: XRAY
Resolution: 2.9 Å
R-factor: N/A
AEROSPACI score: 0.14 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: 3-octaprenyl-4-hydroxybenzoate carboxy-lyase
    Species: Escherichia coli [TaxId:83333]
    Gene: ubiD, b3843
    Database cross-references and differences (RAF-indexed):
    • Uniprot P0AAB4
      • modified residue (59)
      • modified residue (74)
      • modified residue (76)
      • modified residue (119)
      • modified residue (147)
      • modified residue (190)
      • modified residue (381-382)
      • modified residue (392)
      • modified residue (420)
      • modified residue (450)
    Domains in SCOPe 2.08: d2idba1, d2idba2
  • Chain 'B':
    Compound: 3-octaprenyl-4-hydroxybenzoate carboxy-lyase
    Species: Escherichia coli [TaxId:83333]
    Gene: ubiD, b3843
    Database cross-references and differences (RAF-indexed):
    • Uniprot P0AAB4
      • modified residue (59)
      • modified residue (74)
      • modified residue (76)
      • modified residue (119)
      • modified residue (147)
      • modified residue (190)
      • modified residue (381-382)
      • modified residue (392)
      • modified residue (420)
      • modified residue (450)
    Domains in SCOPe 2.08: d2idbb1, d2idbb2
  • Chain 'C':
    Compound: 3-octaprenyl-4-hydroxybenzoate carboxy-lyase
    Species: Escherichia coli [TaxId:83333]
    Gene: ubiD, b3843
    Database cross-references and differences (RAF-indexed):
    • Uniprot P0AAB4
      • modified residue (59)
      • modified residue (74)
      • modified residue (76)
      • modified residue (147)
      • modified residue (190)
      • modified residue (381-382)
      • modified residue (392)
      • modified residue (420)
      • modified residue (450)
    Domains in SCOPe 2.08: d2idbc1, d2idbc2
  • Heterogens: 1PE, EDO, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download) 
    >2idbA (A:)
mdamkyndlrdfltlleqqgelkritlpvdphleiteiadrtlraggpallfenpkgysm
pvlcnlfgtpkrvamgmgqedvsalrevgkllaflkepeppkgfrdlfdklpqfkqvlnm
ptkrlrgapcqqkivsgddvdlnripimtcwpedaaplitwgltvtrgphkerqnlgiyr
qqligknklimrwlshrggaldyqewcaahpgerfpvsvalgadpatilgavtpvpdtls
eyafagllrgtktevvkcisndlevpasaeivlegyieqgetapegpygdhtgyynevds
fpvftvthitqredaiyhstytgrppdepavlgvalnevfvpilqkqfpeivdfylppeg
csyrlavvtikkqyaghakrvmmgvwsflrqfmytkfvivcdddvnardwndviwaittr
mdpardtvlventpidyldfaspvsglgskmgldatnkwpgetqrewgrpikkdpdvvah
idaiwdelaifnngksalehhhhhh

    Sequence, based on observed residues (ATOM records): (download) 
    >2idbA (A:)
yndlrdfltlleqqgelkritlpvdphleiteiadrtlraggpallfenpkgysmpvlcn
lfgtpkrvamgmgqedvsalrevgkllaflkepeppkgfrdlmptkrlrgapcqqkivsg
ddvdlnripimtcwpedaaplitwgltvtrgphkerqnlgiyrqqligknklimrwlshr
ggaldyqewcaahpgerfpvsvalgadpatilgavtpvpdtlseyafagllrgtktevvk
cisndlevpasaeivlegyieqgetapegpygdhtgyynevdsfpvftvthitqredaiy
hstytgrppdepavlgvalnevfvpilqkqfpeivdfylppegcsyrlavvtikkqyagh
akrvmmgvwsflrqfmytkfvivcdddvnardwndviwaittrmdpardtvlventpidy
ldfaspvsglgskmgldatnkwpgetqrewgrpikkdpdvvahidaiwdelaif

  • Chain 'B':
    Sequence, based on SEQRES records: (download) 
    >2idbB (B:)
mdamkyndlrdfltlleqqgelkritlpvdphleiteiadrtlraggpallfenpkgysm
pvlcnlfgtpkrvamgmgqedvsalrevgkllaflkepeppkgfrdlfdklpqfkqvlnm
ptkrlrgapcqqkivsgddvdlnripimtcwpedaaplitwgltvtrgphkerqnlgiyr
qqligknklimrwlshrggaldyqewcaahpgerfpvsvalgadpatilgavtpvpdtls
eyafagllrgtktevvkcisndlevpasaeivlegyieqgetapegpygdhtgyynevds
fpvftvthitqredaiyhstytgrppdepavlgvalnevfvpilqkqfpeivdfylppeg
csyrlavvtikkqyaghakrvmmgvwsflrqfmytkfvivcdddvnardwndviwaittr
mdpardtvlventpidyldfaspvsglgskmgldatnkwpgetqrewgrpikkdpdvvah
idaiwdelaifnngksalehhhhhh

    Sequence, based on observed residues (ATOM records): (download) 
    >2idbB (B:)
ndlrdfltlleqqgelkritlpvdphleiteiadrtlraggpallfenpkgysmpvlcnl
fgtpkrvamgmgqedvsalrevgkllamptkrlrgapcqqkivsgddvdlnripimtcwp
edaaplitwgltvtrgphkerqnlgiyrqqligknklimrwlshrggaldyqewcaahpg
erfpvsvalgadpatilgavtpveyafagllrgtktevvkcisndlevpasaeivlegyi
eqgetapegpygdhtgyynevdsfpvftvthitqredaiyhstytgrppdepavlgvaln
evfvpilqkqfpeivdfylppegcsyrlavvtikkqyaghakrvmmgvwsflrqfmytkf
vivcdddvnardwndviwaittrmdpardtvlventpidyldfaspvsglgskmgldatn
kwpgetqrewgrpikkdpdvvahidaiwdelaifn

  • Chain 'C':
    Sequence, based on SEQRES records: (download) 
    >2idbC (C:)
mdamkyndlrdfltlleqqgelkritlpvdphleiteiadrtlraggpallfenpkgysm
pvlcnlfgtpkrvamgmgqedvsalrevgkllaflkepeppkgfrdlfdklpqfkqvlnm
ptkrlrgapcqqkivsgddvdlnripimtcwpedaaplitwgltvtrgphkerqnlgiyr
qqligknklimrwlshrggaldyqewcaahpgerfpvsvalgadpatilgavtpvpdtls
eyafagllrgtktevvkcisndlevpasaeivlegyieqgetapegpygdhtgyynevds
fpvftvthitqredaiyhstytgrppdepavlgvalnevfvpilqkqfpeivdfylppeg
csyrlavvtikkqyaghakrvmmgvwsflrqfmytkfvivcdddvnardwndviwaittr
mdpardtvlventpidyldfaspvsglgskmgldatnkwpgetqrewgrpikkdpdvvah
idaiwdelaifnngksalehhhhhh

    Sequence, based on observed residues (ATOM records): (download) 
    >2idbC (C:)
kyndlrdfltlleqqgelkritlpvdphleiteiadrtlraggpallfenpkgysmpvlc
nlfgtpkrvamgmgqedvsalrevgkllaflkkrlrgapcqqkivsgddvdlnripimtc
wpedaaplitwgltvtrgphkerqnlgiyrqqligknklimrwlshrggaldyqewcaah
pgerfpvsvalgadpatilgavtpseyafagllrgtktevvkcisndlevpasaeivleg
yieqgetapegpygdhtgyynevdsfpvftvthitqredaiyhstytgrppdepavlgva
lnevfvpilqkqfpeivdfylppegcsyrlavvtikkqyaghakrvmmgvwsflrqfmyt
kfvivcdddvnardwndviwaittrmdpardtvlventpidyldfaspvsglgskmglda
tnkwpgetqrewgrpikkdpdvvahidaiwdelaif