PDB entry 1zq1

View 1zq1 on RCSB PDB site
Description: Structure of GatDE tRNA-Dependent Amidotransferase from Pyrococcus abyssi
Class: lyase
Keywords: x-ray; 3D structure; asparaginase 1 family; GatD subfamily
Deposited on 2005-05-18, released 2005-10-18
The last revision prior to the SCOP 1.73 freeze date was dated 2005-10-18, with a file datestamp of 2007-06-04.
Experiment type: XRAY
Resolution: 3 Å
R-factor: 0.217
AEROSPACI score: 0.22 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: Glutamyl-tRNA(Gln) amidotransferase subunit D
    Species: Pyrococcus abyssi
    Gene: gatD
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q9V0T9 (Start-437)
      • modified residue (35)
      • conflict (126)
      • modified residue (148)
      • modified residue (180)
      • modified residue (190)
      • modified residue (216)
      • modified residue (224)
      • modified residue (233)
      • modified residue (236)
      • modified residue (256)
      • modified residue (361)
      • modified residue (392)
      • modified residue (402)
      • modified residue (417-418)
    Domains in SCOP 1.73: d1zq1a1, d1zq1a2
  • Chain 'B':
    Compound: Glutamyl-tRNA(Gln) amidotransferase subunit D
    Species: Pyrococcus abyssi
    Gene: gatD
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q9V0T9 (Start-437)
      • modified residue (35)
      • conflict (126)
      • modified residue (148)
      • modified residue (180)
      • modified residue (190)
      • modified residue (216)
      • modified residue (224)
      • modified residue (233)
      • modified residue (236)
      • modified residue (256)
      • modified residue (361)
      • modified residue (392)
      • modified residue (402)
      • modified residue (417-418)
    Domains in SCOP 1.73: d1zq1b1, d1zq1b2
  • Chain 'C':
    Compound: Glutamyl-tRNA(Gln) amidotransferase subunit E
    Species: Pyrococcus abyssi
    Gene: gatE
    Database cross-references and differences (RAF-indexed): Domains in SCOP 1.73: d1zq1c1, d1zq1c2, d1zq1c3
  • Chain 'D':
    Compound: Glutamyl-tRNA(Gln) amidotransferase subunit E
    Species: Pyrococcus abyssi
    Gene: gatE
    Database cross-references and differences (RAF-indexed): Domains in SCOP 1.73: d1zq1d1, d1zq1d2, d1zq1d3
  • Heterogens: ASP, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download)
    >1zq1A (A:)
    mrvdeflkerninvgdfvritkeedgeevtyegyimppyelsagdtlvlklengynigia
    lekirrievlerakvkpevhfealiegkpglpevtiigtggtiasridyetgavypafta
    eelakalpeifevanvkpkllfnifsedmkpkhwvkiahevakalnsgdygvvvahgtdt
    mgytaaalsfmlrnlgkpvvlvgaqrssdrpssdaamnlicsvrmatsevaevmvvmhge
    tgdtyclahrgtkvrkmhtsrrdafrsindvpiakiwpngeieflrkdyrkrsdeevevd
    dkieekvalvkvypgisseiidflvdkgykgiviegtglghtpndiipsieraveegvav
    cmtsqciygrvnlnvystgrkllkagvipcedmlpetayvklmwvlghtqnleevrkmml
    tnyageitpytrfdtylr
    

    Sequence, based on observed residues (ATOM records): (download)
    >1zq1A (A:)
    rvdeflkerninvgdfvritkeedgeevtyegyimppyelsagdtlvlklengynigial
    ekirrievlerakvkpevhfealiegkpglpevtiigtggtiasridyetgavypaftae
    elakalpeifevanvkpkllfnifsedmkpkhwvkiahevakalnsgdygvvvahgtdtm
    gytaaalsfmlrnlgkpvvlvgaqrssdrpssdaamnlicsvrmatsevaevmvvmhget
    gdtyclahrgtkvrkmhtsrrdafrsindvpiakiwpngeieflrkdyrkrsdeevevdd
    kieekvalvkvypgisseiidflvdkgykgiviegtglghtpndiipsieraveegvavc
    mtsqciygrvnlnvystgrkllkagvipcedmlpetayvklmwvlghtqnleevrkmmlt
    nyageitpytrfdtylr
    

  • Chain 'B':
    Sequence, based on SEQRES records: (download)
    >1zq1B (B:)
    mrvdeflkerninvgdfvritkeedgeevtyegyimppyelsagdtlvlklengynigia
    lekirrievlerakvkpevhfealiegkpglpevtiigtggtiasridyetgavypafta
    eelakalpeifevanvkpkllfnifsedmkpkhwvkiahevakalnsgdygvvvahgtdt
    mgytaaalsfmlrnlgkpvvlvgaqrssdrpssdaamnlicsvrmatsevaevmvvmhge
    tgdtyclahrgtkvrkmhtsrrdafrsindvpiakiwpngeieflrkdyrkrsdeevevd
    dkieekvalvkvypgisseiidflvdkgykgiviegtglghtpndiipsieraveegvav
    cmtsqciygrvnlnvystgrkllkagvipcedmlpetayvklmwvlghtqnleevrkmml
    tnyageitpytrfdtylr
    

    Sequence, based on observed residues (ATOM records): (download)
    >1zq1B (B:)
    rvdeflkerninvgdfvritkeedgeevtyegyimppyelsagdtlvlklengynigial
    ekirrievlerakvkpevhfealiegkpglpevtiigtggtiasridyetgavypaftae
    elakalpeifevanvkpkllfnifsedmkpkhwvkiahevakalnsgdygvvvahgtdtm
    gytaaalsfmlrnlgkpvvlvgaqrssdrpssdaamnlicsvrmatsevaevmvvmhget
    gdtyclahrgtkvrkmhtsrrdafrsindvpiakiwpngeieflrkdyrkrsdeevevdd
    kieekvalvkvypgisseiidflvdkgykgiviegtglghtpndiipsieraveegvavc
    mtsqciygrvnlnvystgrkllkagvipcedmlpetayvklmwvlghtqnleevrkmmlt
    nyageitpytrfdtylr
    

  • Chain 'C':
    Sequence, based on SEQRES records: (download)
    >1zq1C (C:)
    mmvmtdkfnyeelglkvgleihrqldtkklfspvpselsdkveftfqrrlrptmselgei
    dpaaleefkkgrvyvyegnyeltdlvymdeepprgpdrealevalqiayllnakpvdevy
    ymrkividgsnvsgfqrtaiiatdgkvetpwgavgipticleedaariierkdkeviyrl
    drlgiplieisttpdihhpeqakvvakfigdalratkkvkrglgtirqdlnvsikggari
    eikgvqeldmipiiiereverqlnllkirdelrkrgvkpkdikeefydvtdifentkski
    iarvikkggkvlaiklpkfrgligreiqpgrrlgtefadrakkyvpgifhidelpnygis
    qeevnkvierlnlseedafvlvaaeeekaknalrevikrareaiegvpeetrralpdgnt
    eymrplpgkarmypetdipplripddlkkkikenlpelpqakveryvkeykldrslaqtl
    vdderdelfeelvsmgvkpslaasilvvvlkglrkevpienvtdehireafqlylegkia
    keafeeifkelarnpsksarevaeekgltllseeevtriieeviqqnievvkakgmgamg
    limgrvmakvrgkadgklvsqivrrklqeisgg
    

    Sequence, based on observed residues (ATOM records): (download)
    >1zq1C (C:)
    tdkfnyeelglkvgleihrqldtkklfspvpselsdkveftfqrrlrptmselgeidpaa
    leefkkgrvyvyegnyeltdlvymdeepprgpdrealevalqiayllnakpvdevyymrk
    ividgsnvsgfqrtaiiatdgkvetpwgavgipticleedaariierkdkeviyrldrlg
    iplieisttpdihhpeqakvvakfigdalratkkvkrglgtirqdlnvsikggarieikg
    vqeldmipiiiereverqlnllkirdelrkrgvkpkdikeefydvtdifentkskiiarv
    ikkggkvlaiklpkfrgligreiqpgrrlgtefadrakkyvpgifhidelpnygisqeev
    nkvierlnlseedafvlvaaeeekaknalrevikrareaiegvpeetrralpdgnteymr
    plpgkarmypetdipplripddlkkkikenlpelpqakveryvkeykldrslaqtlvdde
    rdelfeelvsmgvkpslaasilvvvlkg
    

  • Chain 'D':
    Sequence, based on SEQRES records: (download)
    >1zq1D (D:)
    mmvmtdkfnyeelglkvgleihrqldtkklfspvpselsdkveftfqrrlrptmselgei
    dpaaleefkkgrvyvyegnyeltdlvymdeepprgpdrealevalqiayllnakpvdevy
    ymrkividgsnvsgfqrtaiiatdgkvetpwgavgipticleedaariierkdkeviyrl
    drlgiplieisttpdihhpeqakvvakfigdalratkkvkrglgtirqdlnvsikggari
    eikgvqeldmipiiiereverqlnllkirdelrkrgvkpkdikeefydvtdifentkski
    iarvikkggkvlaiklpkfrgligreiqpgrrlgtefadrakkyvpgifhidelpnygis
    qeevnkvierlnlseedafvlvaaeeekaknalrevikrareaiegvpeetrralpdgnt
    eymrplpgkarmypetdipplripddlkkkikenlpelpqakveryvkeykldrslaqtl
    vdderdelfeelvsmgvkpslaasilvvvlkglrkevpienvtdehireafqlylegkia
    keafeeifkelarnpsksarevaeekgltllseeevtriieeviqqnievvkakgmgamg
    limgrvmakvrgkadgklvsqivrrklqeisgg
    

    Sequence, based on observed residues (ATOM records): (download)
    >1zq1D (D:)
    tdkfnyeelglkvgleihrqldtkklfspvpselsdkveftfqrrlrptmselgeidpaa
    leefkkgrvyvyegnyeltdlvymdeepprgpdrealevalqiayllnakpvdevyymrk
    ividgsnvsgfqrtaiiatdgkvetpwgavgipticleedaariierkdkeviyrldrlg
    iplieisttpdihhpeqakvvakfigdalratkkvkrglgtirqdlnvsikggarieikg
    vqeldmipiiiereverqlnllkirdelrkrgvkpkdikeefydvtdifentkskiiarv
    ikkggkvlaiklpkfrgligreiqpgrrlgtefadrakkyvpgifhidelpnygisqeev
    nkvierlnlseedafvlvaaeeekaknalrevikrareaiegvpeetrralpdgnteymr
    plpgkarmypetdipplripddlkkkikenlpelpqakveryvkeykldrslaqtlvdde
    rdelfeelvsmgvkpslaasilvvvlkg