PDB entry 6mdy

View 6mdy on RCSB PDB site
Description: Crystal structure of a 2-dehydro-3-deoxyphosphooctonate aldolase from Legionella pneumophila Philadelphia 1
Class: hydrolase
Keywords: NIAID, structural genomics, aldolase, phosphoenolpyruvate, D-arabinose 5-phosphate, 3-deoxy-D-manno-octulosonate 8-phosphate, Seattle Structural Genomics Center for Infectious Disease, SSGCID, HYDROLASE
Deposited on 2018-09-05, released 2018-09-19
The last revision prior to the SCOPe 2.07 freeze date was dated 2018-09-19, with a file datestamp of 2018-09-14.
Experiment type: XRAY
Resolution: 2.55 Å
R-factor: N/A
AEROSPACI score: 0.2 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: 2-dehydro-3-deoxyphosphooctonate aldolase
    Species: Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513) [TaxId:272624]
    Gene: kdsA, lpg1182
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q5ZWA3 (8-281)
      • expression tag (7)
    Domains in SCOPe 2.07: d6mdya1, d6mdya2
  • Chain 'B':
    Compound: 2-dehydro-3-deoxyphosphooctonate aldolase
    Species: Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513) [TaxId:272624]
    Gene: kdsA, lpg1182
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q5ZWA3 (8-281)
      • expression tag (7)
    Domains in SCOPe 2.07: d6mdyb1, d6mdyb2
  • Chain 'C':
    Compound: 2-dehydro-3-deoxyphosphooctonate aldolase
    Species: Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513) [TaxId:272624]
    Gene: kdsA, lpg1182
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q5ZWA3 (8-281)
      • expression tag (7)
    Domains in SCOPe 2.07: d6mdyc1, d6mdyc2
  • Chain 'D':
    Compound: 2-dehydro-3-deoxyphosphooctonate aldolase
    Species: Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513) [TaxId:272624]
    Gene: kdsA, lpg1182
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q5ZWA3 (8-281)
      • expression tag (6-7)
    Domains in SCOPe 2.07: d6mdyd1, d6mdyd2
  • Heterogens: HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download)
    >6mdyA (A:)
    mahhhhhhmrlcgfeagldkplfliagpcvieseelaletagylkemcsqlnipfiykss
    fdkanrssissyrgpgfekglsilekvksqigvpvltdvhedtplfevssvvdvlqtpaf
    lcrqtnfiqkvaamnkpvnikkgqflapwemkhviakakaqgneqimacergvsfgynnl
    vsdmrslvimretgcpvvydathsvqlpggnngvsggqrefipalaraavavgisglfme
    thpdpdkalsdgpnswpldkmkqlleslkaadevykkystdf
    

    Sequence, based on observed residues (ATOM records): (download)
    >6mdyA (A:)
    hmrlcgfeagldkplfliagpcvieseelaletagylkemcsqlnipfiykssfpgfekg
    lsilekvksqigvpvltdvhedtplfevssvvdvlqtpaflcrqtnfiqkvaamnkpvni
    kkgqflapwemkhviakakaqgneqimacergvsfgynnlvsdmrslvimretgcpvvyd
    athsvqqrefipalaraavavgisglfmethppnswpldkmkqlleslkaadevykkyst
    df
    

  • Chain 'B':
    Sequence, based on SEQRES records: (download)
    >6mdyB (B:)
    mahhhhhhmrlcgfeagldkplfliagpcvieseelaletagylkemcsqlnipfiykss
    fdkanrssissyrgpgfekglsilekvksqigvpvltdvhedtplfevssvvdvlqtpaf
    lcrqtnfiqkvaamnkpvnikkgqflapwemkhviakakaqgneqimacergvsfgynnl
    vsdmrslvimretgcpvvydathsvqlpggnngvsggqrefipalaraavavgisglfme
    thpdpdkalsdgpnswpldkmkqlleslkaadevykkystdf
    

    Sequence, based on observed residues (ATOM records): (download)
    >6mdyB (B:)
    hmrlcgfeagldkplfliagpcvieseelaletagylkemcsqlnipfiykssfgpgfek
    glsilekvksqigvpvltdvhedtplfevssvvdvlqtpaflcrqtnfiqkvaamnkpvn
    ikkgqflapwemkhviakakaqgneqimacergvsfgynnlvsdmrslvimretgcpvvy
    dathsvqqrefipalaraavavgisglfmethpnswpldkmkqlleslkaadevykkyst
    df
    

  • Chain 'C':
    Sequence, based on SEQRES records: (download)
    >6mdyC (C:)
    mahhhhhhmrlcgfeagldkplfliagpcvieseelaletagylkemcsqlnipfiykss
    fdkanrssissyrgpgfekglsilekvksqigvpvltdvhedtplfevssvvdvlqtpaf
    lcrqtnfiqkvaamnkpvnikkgqflapwemkhviakakaqgneqimacergvsfgynnl
    vsdmrslvimretgcpvvydathsvqlpggnngvsggqrefipalaraavavgisglfme
    thpdpdkalsdgpnswpldkmkqlleslkaadevykkystdf
    

    Sequence, based on observed residues (ATOM records): (download)
    >6mdyC (C:)
    hmrlcgfeagldkplfliagpcvieseelaletagylkemcsqlnipfiykssffekgls
    ilekvksqigvpvltdvhedtplfevssvvdvlqtpaflcrqtnfiqkvaamnkpvnikk
    gqflapwemkhviakakaqgneqimacergvsfgynnlvsdmrslvimretgcpvvydat
    hsvqqrefipalaraavavgisglfmethpnswpldkmkqlleslkaadevykkystdf
    

  • Chain 'D':
    Sequence, based on SEQRES records: (download)
    >6mdyD (D:)
    mahhhhhhmrlcgfeagldkplfliagpcvieseelaletagylkemcsqlnipfiykss
    fdkanrssissyrgpgfekglsilekvksqigvpvltdvhedtplfevssvvdvlqtpaf
    lcrqtnfiqkvaamnkpvnikkgqflapwemkhviakakaqgneqimacergvsfgynnl
    vsdmrslvimretgcpvvydathsvqlpggnngvsggqrefipalaraavavgisglfme
    thpdpdkalsdgpnswpldkmkqlleslkaadevykkystdf
    

    Sequence, based on observed residues (ATOM records): (download)
    >6mdyD (D:)
    hhmrlcgfeagldkplfliagpcvieseelaletagylkemcsqlnipfiykssfdkanr
    ssissyrgpgfekglsilekvksqigvpvltdvhedtplfevssvvdvlqtpaflcrqtn
    fiqkvaamnkpvnikkgqflapwemkhviakakaqgneqimacergvsfgynnlvsdmrs
    lvimretgcpvvydathsvqqrefipalaraavavgisglfmethpnswpldkmkqlles
    lkaadevykkystdf