PDB entry 4dpg

View 4dpg on RCSB PDB site
Description: Crystal Structure of Human LysRS: P38/AIMP2 Complex I
Class: Ligase/APOPTOSIS
Keywords: lysyl-tRNA synthetase, LysRS, P38, AIMP2, multi tRNA synthetase complex sub-complex, Ligase-APOPTOSIS complex
Deposited on 2012-02-13, released 2013-02-13
The last revision prior to the SCOPe 2.05 freeze date was dated 2013-02-13, with a file datestamp of 2013-02-08.
Experiment type: XRAY
Resolution: 2.84 Å
R-factor: 0.187
AEROSPACI score: 0.28 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: Lysine--tRNA ligase
    Species: Homo sapiens [TaxId:9606]
    Gene: KARS, KIAA0070
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.05: d4dpga1, d4dpga2
  • Chain 'B':
    Compound: Lysine--tRNA ligase
    Species: Homo sapiens [TaxId:9606]
    Gene: KARS, KIAA0070
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.05: d4dpgb1, d4dpgb2
  • Chain 'C':
    Compound: Lysine--tRNA ligase
    Species: Homo sapiens [TaxId:9606]
    Gene: KARS, KIAA0070
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.05: d4dpgc1, d4dpgc2
  • Chain 'D':
    Compound: Lysine--tRNA ligase
    Species: Homo sapiens [TaxId:9606]
    Gene: KARS, KIAA0070
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.05: d4dpgd1, d4dpgd2
  • Chain 'E':
    Compound: Lysine--tRNA ligase
    Species: Homo sapiens [TaxId:9606]
    Gene: KARS, KIAA0070
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.05: d4dpge1, d4dpge2
  • Chain 'F':
    Compound: Lysine--tRNA ligase
    Species: Homo sapiens [TaxId:9606]
    Gene: KARS, KIAA0070
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.05: d4dpgf1, d4dpgf2
  • Chain 'G':
    Compound: Lysine--tRNA ligase
    Species: Homo sapiens [TaxId:9606]
    Gene: KARS, KIAA0070
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.05: d4dpgg1, d4dpgg2
  • Chain 'H':
    Compound: Lysine--tRNA ligase
    Species: Homo sapiens [TaxId:9606]
    Gene: KARS, KIAA0070
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.05: d4dpgh1, d4dpgh2
  • Chain 'I':
    Compound: Aminoacyl tRNA synthase complex-interacting multifunctional protein 2
    Species: Homo sapiens [TaxId:9606]
    Gene: AIMP2, JTV1, PRO0992
    Database cross-references and differences (RAF-indexed):
  • Chain 'J':
    Compound: Aminoacyl tRNA synthase complex-interacting multifunctional protein 2
    Species: Homo sapiens [TaxId:9606]
    Gene: AIMP2, JTV1, PRO0992
    Database cross-references and differences (RAF-indexed):
  • Chain 'K':
    Compound: Aminoacyl tRNA synthase complex-interacting multifunctional protein 2
    Species: Homo sapiens [TaxId:9606]
    Gene: AIMP2, JTV1, PRO0992
    Database cross-references and differences (RAF-indexed):
  • Chain 'L':
    Compound: Aminoacyl tRNA synthase complex-interacting multifunctional protein 2
    Species: Homo sapiens [TaxId:9606]
    Gene: AIMP2, JTV1, PRO0992
    Database cross-references and differences (RAF-indexed):
  • Heterogens: LYS, APC, MG, ALA, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download)
    >4dpgA (A:)
    msvdpnqyykirsqaihqlkvngedpyphkfhvdisltdfiqkyshlqpgdhltditlkv
    agrihakrasggklifydlrgegvklqvmansrnykseeefihinnklrrgdiigvqgnp
    gktkkgelsiipyeitllspclhmlphlhfglkdketryrqryldlilndfvrqkfiirs
    kiityirsfldelgfleietpmmniipggavakpfityhneldmnlymriapelyhkmlv
    vggidrvyeigrqfrnegidlthnpefttcefymayadyhdlmeitekmvsgmvkhitgs
    ykvtyhpdgpegqaydvdftppfrrinmveelekalgmklpetnlfeteetrkilddicv
    akavecppprttarlldklvgeflevtcinptficdhpqimsplakwhrskeglterfel
    fvmkkeicnaytelndpmrqrqlfeeqakakaagddeamfidenfctaleyglpptagwg
    mgidrvamfltdsnnikevllfpamkpedkken
    

    Sequence, based on observed residues (ATOM records): (download)
    >4dpgA (A:)
    vdpnqyykirsqaihqlkvngedpyphkfhvdisltdfiqkyshlqpgdhltditlkvag
    rihakrasggklifydlrgegvklqvmansrnykseeefihinnklrrgdiigvqgnpgk
    tkkgelsiipyeitllspclhmlphlkdketryrqryldlilndfvrqkfiirskiityi
    rsfldelgfleietpmmniipggavakpfityhneldmnlymriapelyhkmlvvggidr
    vyeigrqfrnegidlthnpefttcefymayadyhdlmeitekmvsgmvkhitgsykvtyh
    pdgpegqaydvdftppfrrinmveelekalgmklpetnlfeteetrkilddicvakavec
    ppprttarlldklvgeflevtcinptficdhpqimsplakwhrskeglterfelfvmkke
    icnaytelndpmrqrqlfeeqakakaagddeamfidenfctaleyglpptagwgmgidrv
    amfltdsnnikevllfpamkp
    

  • Chain 'B':
    Sequence, based on SEQRES records: (download)
    >4dpgB (B:)
    msvdpnqyykirsqaihqlkvngedpyphkfhvdisltdfiqkyshlqpgdhltditlkv
    agrihakrasggklifydlrgegvklqvmansrnykseeefihinnklrrgdiigvqgnp
    gktkkgelsiipyeitllspclhmlphlhfglkdketryrqryldlilndfvrqkfiirs
    kiityirsfldelgfleietpmmniipggavakpfityhneldmnlymriapelyhkmlv
    vggidrvyeigrqfrnegidlthnpefttcefymayadyhdlmeitekmvsgmvkhitgs
    ykvtyhpdgpegqaydvdftppfrrinmveelekalgmklpetnlfeteetrkilddicv
    akavecppprttarlldklvgeflevtcinptficdhpqimsplakwhrskeglterfel
    fvmkkeicnaytelndpmrqrqlfeeqakakaagddeamfidenfctaleyglpptagwg
    mgidrvamfltdsnnikevllfpamkpedkken
    

    Sequence, based on observed residues (ATOM records): (download)
    >4dpgB (B:)
    vdpnqyykirsqaihqlkvngedpyphkfhvdisltdfiqkyshlqpgdhltditlkvag
    rihakrasggklifydlrgegvklqvmansrnykseeefihinnklrrgdiigvqgnpgk
    tkkgelsiipyeitllspclhmlphlhfglkdketryrqryldlilndfvrqkfiirski
    ityirsfldelgfleietpmmniipggavakpfityhneldmnlymriapelyhkmlvvg
    gidrvyeigrqfrnegidlthnpefttcefymayadyhdlmeitekmvsgmvkhitgsyk
    vtyhpdgpegqaydvdftppfrrinmveelekalgmklpetnlfeteetrkilddicvak
    avecppprttarlldklvgeflevtcinptficdhpqimsplakwhrskeglterfelfv
    mkkeicnaytelndpmrqrqlfeeqakakaagddeamfidenfctaleyglpptagwgmg
    idrvamfltdsnnikevllfpamkpe
    

  • Chain 'C':
    Sequence, based on SEQRES records: (download)
    >4dpgC (C:)
    msvdpnqyykirsqaihqlkvngedpyphkfhvdisltdfiqkyshlqpgdhltditlkv
    agrihakrasggklifydlrgegvklqvmansrnykseeefihinnklrrgdiigvqgnp
    gktkkgelsiipyeitllspclhmlphlhfglkdketryrqryldlilndfvrqkfiirs
    kiityirsfldelgfleietpmmniipggavakpfityhneldmnlymriapelyhkmlv
    vggidrvyeigrqfrnegidlthnpefttcefymayadyhdlmeitekmvsgmvkhitgs
    ykvtyhpdgpegqaydvdftppfrrinmveelekalgmklpetnlfeteetrkilddicv
    akavecppprttarlldklvgeflevtcinptficdhpqimsplakwhrskeglterfel
    fvmkkeicnaytelndpmrqrqlfeeqakakaagddeamfidenfctaleyglpptagwg
    mgidrvamfltdsnnikevllfpamkpedkken
    

    Sequence, based on observed residues (ATOM records): (download)
    >4dpgC (C:)
    vdpnqyykirsqaihqlkvngedpyphkfhvdisltdfiqkyshlqpgdhltditlkvag
    rihakrasggklifydlrgegvklqvmansrnykseeefihinnklrrgdiigvqgnpgk
    tkkgelsiipyeitllspclhmlphlkdketryrqryldlilndfvrqkfiirskiityi
    rsfldelgfleietpmmniipggavakpfityhneldmnlymriapelyhkmlvvggidr
    vyeigrqfrnegidlthnpefttcefymayadyhdlmeitekmvsgmvkhitgsykvtyh
    pdgpegqaydvdftppfrrinmveelekalgmklpetnlfeteetrkilddicvakavec
    ppprttarlldklvgeflevtcinptficdhpqimsplakwhrskeglterfelfvmkke
    icnaytelndpmrqrqlfeeqakakaagddeamfidenfctaleyglpptagwgmgidrv
    amfltdsnnikevllfpamkp
    

  • Chain 'D':
    Sequence, based on SEQRES records: (download)
    >4dpgD (D:)
    msvdpnqyykirsqaihqlkvngedpyphkfhvdisltdfiqkyshlqpgdhltditlkv
    agrihakrasggklifydlrgegvklqvmansrnykseeefihinnklrrgdiigvqgnp
    gktkkgelsiipyeitllspclhmlphlhfglkdketryrqryldlilndfvrqkfiirs
    kiityirsfldelgfleietpmmniipggavakpfityhneldmnlymriapelyhkmlv
    vggidrvyeigrqfrnegidlthnpefttcefymayadyhdlmeitekmvsgmvkhitgs
    ykvtyhpdgpegqaydvdftppfrrinmveelekalgmklpetnlfeteetrkilddicv
    akavecppprttarlldklvgeflevtcinptficdhpqimsplakwhrskeglterfel
    fvmkkeicnaytelndpmrqrqlfeeqakakaagddeamfidenfctaleyglpptagwg
    mgidrvamfltdsnnikevllfpamkpedkken
    

    Sequence, based on observed residues (ATOM records): (download)
    >4dpgD (D:)
    vdpnqyykirsqaihqlkvngedpyphkfhvdisltdfiqkyshlqpgdhltditlkvag
    rihakrasggklifydlrgegvklqvmansrnykseeefihinnklrrgdiigvqgnpgk
    tkkgelsiipyeitllspclhmlphlhfglkdketryrqryldlilndfvrqkfiirski
    ityirsfldelgfleietpmmniipggavakpfityhneldmnlymriapelyhkmlvvg
    gidrvyeigrqfrnegidlthnpefttcefymayadyhdlmeitekmvsgmvkhitgsyk
    vtyhpdgpegqaydvdftppfrrinmveelekalgmklpetnlfeteetrkilddicvak
    avecppprttarlldklvgeflevtcinptficdhpqimsplakwhrskeglterfelfv
    mkkeicnaytelndpmrqrqlfeeqakakaagddeamfidenfctaleyglpptagwgmg
    idrvamfltdsnnikevllfpamkp
    

  • Chain 'E':
    Sequence, based on SEQRES records: (download)
    >4dpgE (E:)
    msvdpnqyykirsqaihqlkvngedpyphkfhvdisltdfiqkyshlqpgdhltditlkv
    agrihakrasggklifydlrgegvklqvmansrnykseeefihinnklrrgdiigvqgnp
    gktkkgelsiipyeitllspclhmlphlhfglkdketryrqryldlilndfvrqkfiirs
    kiityirsfldelgfleietpmmniipggavakpfityhneldmnlymriapelyhkmlv
    vggidrvyeigrqfrnegidlthnpefttcefymayadyhdlmeitekmvsgmvkhitgs
    ykvtyhpdgpegqaydvdftppfrrinmveelekalgmklpetnlfeteetrkilddicv
    akavecppprttarlldklvgeflevtcinptficdhpqimsplakwhrskeglterfel
    fvmkkeicnaytelndpmrqrqlfeeqakakaagddeamfidenfctaleyglpptagwg
    mgidrvamfltdsnnikevllfpamkpedkken
    

    Sequence, based on observed residues (ATOM records): (download)
    >4dpgE (E:)
    dpnqyykirsqaihqlkvngedpyphkfhvdisltdfiqkyshlqpgdhltditlkvagr
    ihakrasggklifydlrgegvklqvmansrnykseeefihinnklrrgdiigvqgnpgkt
    kkgelsiipyeitllspclhmlphlkdketryrqryldlilndfvrqkfiirskiityir
    sfldelgfleietpmmniipggavakpfityhneldmnlymriapelyhkmlvvggidrv
    yeigrqfrnegidlthnpefttcefymayadyhdlmeitekmvsgmvkhitgsykvtyhp
    dgpegqaydvdftppfrrinmveelekalgmklpetnlfeteetrkilddicvakavecp
    pprttarlldklvgeflevtcinptficdhpqimsplakwhrskeglterfelfvmkkei
    cnaytelndpmrqrqlfeeqakakaagddeamfidenfctaleyglpptagwgmgidrva
    mfltdsnnikevllfpamkp
    

  • Chain 'F':
    Sequence, based on SEQRES records: (download)
    >4dpgF (F:)
    msvdpnqyykirsqaihqlkvngedpyphkfhvdisltdfiqkyshlqpgdhltditlkv
    agrihakrasggklifydlrgegvklqvmansrnykseeefihinnklrrgdiigvqgnp
    gktkkgelsiipyeitllspclhmlphlhfglkdketryrqryldlilndfvrqkfiirs
    kiityirsfldelgfleietpmmniipggavakpfityhneldmnlymriapelyhkmlv
    vggidrvyeigrqfrnegidlthnpefttcefymayadyhdlmeitekmvsgmvkhitgs
    ykvtyhpdgpegqaydvdftppfrrinmveelekalgmklpetnlfeteetrkilddicv
    akavecppprttarlldklvgeflevtcinptficdhpqimsplakwhrskeglterfel
    fvmkkeicnaytelndpmrqrqlfeeqakakaagddeamfidenfctaleyglpptagwg
    mgidrvamfltdsnnikevllfpamkpedkken
    

    Sequence, based on observed residues (ATOM records): (download)
    >4dpgF (F:)
    vdpnqyykirsqaihqlkvngedpyphkfhvdisltdfiqkyshlqpgdhltditlkvag
    rihakrasggklifydlrgegvklqvmansrnykseeefihinnklrrgdiigvqgnpgk
    tkkgelsiipyeitllspclhmlphlhfglkdketryrqryldlilndfvrqkfiirski
    ityirsfldelgfleietpmmniipggavakpfityhneldmnlymriapelyhkmlvvg
    gidrvyeigrqfrnegidlthnpefttcefymayadyhdlmeitekmvsgmvkhitgsyk
    vtyhpdgpegqaydvdftppfrrinmveelekalgmklpetnlfeteetrkilddicvak
    avecppprttarlldklvgeflevtcinptficdhpqimsplakwhrskeglterfelfv
    mkkeicnaytelndpmrqrqlfeeqakakaagddeamfidenfctaleyglpptagwgmg
    idrvamfltdsnnikevllfpamkp
    

  • Chain 'G':
    Sequence, based on SEQRES records: (download)
    >4dpgG (G:)
    msvdpnqyykirsqaihqlkvngedpyphkfhvdisltdfiqkyshlqpgdhltditlkv
    agrihakrasggklifydlrgegvklqvmansrnykseeefihinnklrrgdiigvqgnp
    gktkkgelsiipyeitllspclhmlphlhfglkdketryrqryldlilndfvrqkfiirs
    kiityirsfldelgfleietpmmniipggavakpfityhneldmnlymriapelyhkmlv
    vggidrvyeigrqfrnegidlthnpefttcefymayadyhdlmeitekmvsgmvkhitgs
    ykvtyhpdgpegqaydvdftppfrrinmveelekalgmklpetnlfeteetrkilddicv
    akavecppprttarlldklvgeflevtcinptficdhpqimsplakwhrskeglterfel
    fvmkkeicnaytelndpmrqrqlfeeqakakaagddeamfidenfctaleyglpptagwg
    mgidrvamfltdsnnikevllfpamkpedkken
    

    Sequence, based on observed residues (ATOM records): (download)
    >4dpgG (G:)
    dpnqyykirsqaihqlkvngedpyphkfhvdisltdfiqkyshlqpgdhltditlkvagr
    ihakrasggklifydlrgegvklqvmansrnykseeefihinnklrrgdiigvqgnpgkt
    kkgelsiipyeitllspclhmlphglkdketryrqryldlilndfvrqkfiirskiityi
    rsfldelgfleietpmmniipggavakpfityhneldmnlymriapelyhkmlvvggidr
    vyeigrqfrnegidlthnpefttcefymayadyhdlmeitekmvsgmvkhitgsykvtyh
    pdgpegqaydvdftppfrrinmveelekalgmklpetnlfeteetrkilddicvakavec
    ppprttarlldklvgeflevtcinptficdhpqimsplakwhrskeglterfelfvmkke
    icnaytelndpmrqrqlfeeqakakaagddeamfidenfctaleyglpptagwgmgidrv
    amfltdsnnikevllfpamkp
    

  • Chain 'H':
    Sequence, based on SEQRES records: (download)
    >4dpgH (H:)
    msvdpnqyykirsqaihqlkvngedpyphkfhvdisltdfiqkyshlqpgdhltditlkv
    agrihakrasggklifydlrgegvklqvmansrnykseeefihinnklrrgdiigvqgnp
    gktkkgelsiipyeitllspclhmlphlhfglkdketryrqryldlilndfvrqkfiirs
    kiityirsfldelgfleietpmmniipggavakpfityhneldmnlymriapelyhkmlv
    vggidrvyeigrqfrnegidlthnpefttcefymayadyhdlmeitekmvsgmvkhitgs
    ykvtyhpdgpegqaydvdftppfrrinmveelekalgmklpetnlfeteetrkilddicv
    akavecppprttarlldklvgeflevtcinptficdhpqimsplakwhrskeglterfel
    fvmkkeicnaytelndpmrqrqlfeeqakakaagddeamfidenfctaleyglpptagwg
    mgidrvamfltdsnnikevllfpamkpedkken
    

    Sequence, based on observed residues (ATOM records): (download)
    >4dpgH (H:)
    vdpnqyykirsqaihqlkvngedpyphkfhvdisltdfiqkyshlqpgdhltditlkvag
    rihakrasggklifydlrgegvklqvmansrnykseeefihinnklrrgdiigvqgnpgk
    tkkgelsiipyeitllspclhmlphlhfglkdketryrqryldlilndfvrqkfiirski
    ityirsfldelgfleietpmmniipggavakpfityhneldmnlymriapelyhkmlvvg
    gidrvyeigrqfrnegidlthnpefttcefymayadyhdlmeitekmvsgmvkhitgsyk
    vtyhpdgpegqaydvdftppfrrinmveelekalgmklpetnlfeteetrkilddicvak
    avecppprttarlldklvgeflevtcinptficdhpqimsplakwhrskeglterfelfv
    mkkeicnaytelndpmrqrqlfeeqakakaagddeamfidenfctaleyglpptagwgmg
    idrvamfltdsnnikevllfpamkp
    

  • Chain 'I':
    No sequence available.

  • Chain 'J':
    No sequence available.

  • Chain 'K':
    No sequence available.

  • Chain 'L':
    No sequence available.